(reformed answer)

1. Same origin

If you have one <iframe>that has the same origin as your domain, no problem, you can do something simple like:

iframe.contentWindow.document

In this way we obtain the window contained in the<iframe>

1.1 - Getting the links

We can simply do a querySelectorAll, so that we will obtain those <a>of the document of the<iframe>

iframe.contentWindow.document.querySelectorAll("a");

Once we have obtained all the links, we can simply do adisplay: none

iframe.contentWindow.document.querySelectorAll("a").forEach(el => {
    el.style.display = "none";
});;

1.2 - Integration with localStorage

You can add an eventListener to the window, so we will define a function and when the window loads we will call it, it will get all the links of the <iframe>, we will add a unique index to each link, so that we can recognize each one in localStorage, we will add an eventListener to Each link, when clicking, will check if the number of clicks is greater than or equal to the one defined in the max constant , if it is greater than or equal, we will do a preventDefault so that it will no longer redirect

const cargarLinksStorage = () => {
  const max = 1; // Número máximo de clicks por link
  let iframe = document.querySelector("iframe");
  let elmnt = iframe.contentWindow.document.querySelectorAll("A");
  for(i = 0;i<elmnt.length;i++) {
    if (localStorage.getItem("link"+i) == null){localStorage.setItem("link"+i, "0")}
    elmnt[i].linkPos = i;
    elmnt[i].addEventListener("click", function(e) {
        if (localStorage.getItem("link"+this.linkPos) >= max){
            e.preventDefault();
        } else {
            localStorage.setItem("link"+this.linkPos, parseInt(localStorage.getItem("link"+this.linkPos))+1)
        }
    }); }
}

window.addEventListener("load", () => {
    cargarLinksStorage();
});

1.3 - Expiration date

We can save the last day in the month (From 1 to 30 / From 1 to 31)

So we'll get today's day in a month (Same way: 1 - 30 / 1 - 31) And compare it to the date stored in localStorage , subtract both dates, the result, mathematically:

• It will give a positive number if the term is 48 hours and has not expired
• It will give a negative number if the term is 48 hours and it has expired
• It will give a positive number starting from 1 if the term is 24 hours and has not expired
• It will give a negative number starting from 0 if the term is 24 hours and has expired

So we have the following code:

window.addEventListener("load", () => {
    cargarLinksStorage();
    let archive = {}, // Notice change here
    keys = Object.keys(localStorage),
    i = keys.length;
    while ( i-- ) {
        archive[ keys[i] ] = localStorage.getItem( keys[i] );
    }
    Object.entries(archive).forEach(entry => {
        const [key,value] = entry;
        if (key.includes("link")) {
            if (localStorage.getItem("lastDate") !== null && parseInt(localStorage.getItem("lastDate")) - new Date().getDate() < -1) { // 0 para 1 día y -1 para 2 días
                localStorage.setItem(key, 0);
                localStorage.setItem("lastDate", new Date().getDate())
            }
        }
    })
    if (localStorage.getItem("lastDate") == null) {
        localStorage.setItem("lastDate", new Date().getDate())
    }
});

it is important that that expiration function works for this online user or not.

This cannot be done, if the user has not loaded the page, this cannot be done, the user will have to load the page for the scripts to run

2. Different origins

When we work with <iframe>from different origins, it will not be possible to access the DOM of this, due to security reasons, if we try to do a contentWindow.document, it will give you the following error

Access to cross-origin frame has been blocked due to CORS Policy

To fix this we can simply create an <div>invisible and have it show if the click counter has exceeded 3 clicks

let i = 0;
const max = 2; // Número máximo de click por cada anuncio
window.addEventListener("load", () => {
  document.querySelectorAll(".ads").forEach(el => {
    if (parseInt(localStorage.getItem("ad"+i)) >= max) {
      el.innerHTML = `<div class="invDiv"></div>${el.innerHTML}`;
    }
    el.addEventListener("click", () => {
       if (localStorage.getItem("ad"+i) == null) {
          localStorage.setItem("ad"+i, "0");
       } else {
          localStorage.setItem("ad"+i, parseInt(localStorage.getItem("ad"+i))+1)
       }
    });
    i++;
  });
});

In addition, apply the following styles, so that the <div>invisible one can be superimposed on <iframe>it and it cannot be clicked

/* Estilos necesarios */

.ads {
  position:relative;
}

.invDiv {
  position:absolute;
  height:100%;
  width:100%;
  z-index:20;
}

2.1 - Demonstration

window.addEventListener("load", () => {
  document.querySelectorAll(".ads").forEach(el => {
    el.innerHTML = `<div class="invDiv"></div>${el.innerHTML}`;
  });
});

/* Estilos no necesarios con iFrame */

.iframe {
  height:200px;
  width:200px;
  border:2px solid red;
}

.iframe > a {
  font-size:6rem;
}

/* END Estilos no necesarios /*

/* Estilos necesarios */

.ads {
  position:relative;
}

.invDiv {
  position:absolute;
  height:100%;
  width:100%;
  z-index:20;
}

<div class="ads">
  <div class="iframe"><a href="https://es.stackoverflow.com/">SOes</a></div>
</div>

<!-- Vamos a simular que el div de clase "iframe" es tu iframe -->

As you can see, the link is no longer clickable. We add, using javascript, a <div>when the window loads

2.2 - Expiration date

The method is also similar

window.addEventListener("load", () => {
    let archive = {}, // Notice change here
    keys = Object.keys(localStorage),
    i = keys.length;
    while ( i-- ) {
        archive[ keys[i] ] = localStorage.getItem( keys[i] );
    }
    Object.entries(archive).forEach(entry => {
        const [key,value] = entry;
        if (key.includes("ad")) {
            if (localStorage.getItem("lastDate") !== null && parseInt(localStorage.getItem("lastDate")) - new Date().getDate() < -1) { // 0 para 1 día y -1 para 2 días
                localStorage.setItem(key, 0);
                localStorage.setItem("lastDate", new Date().getDate())
            }
        }
    })
    if (localStorage.getItem("lastDate") == null) {
        localStorage.setItem("lastDate", new Date().getDate())
    }
});

You can use a bit of ingenuity to get a click counter on iframes. Even if these are protected by CORS restrictions (origins other than your domain).

This is because, even for cross-origin access, the browser needs minimal communication between windows or frames.

By keeping focus on our main window, we can capture when we lose focus from it (in favor of the iframe the user clicked on) and assess whether the last active element on our site was the iframe we were looking for.

At this point it is important to bring the focus back to the main window ( invisible to the user ) in order to detect several clicks in a row.

I leave you a little developed the theory. If you have any doubt to implement it, do not hesitate to consult.

Update 01/21/2021, persistence in localStorage

Version with persistence. For reasons of restriction of use of localstorage in stackoverflow. Attached example in jsfiddle :

const adsProtector = {
  limit : 3,
  current : 0,
  expiration : 60,
  query : '.ads > iframe',
  init : function(){
    const $ = (...args) => document.querySelectorAll(...args);
    let self = this;

    // Persistencia
    let adsProtectorSession = JSON.parse(localStorage.getItem('adsProtectorSession'));
    adsProtectorSession = (adsProtectorSession.timestamp) ? adsProtectorSession : self._sessionObj();
    self.current = adsProtectorSession.current;

    window.focus();
    self.$frames = $('.ads > iframe');
    self.$frames.forEach(($frame)=>{
      window.addEventListener('blur', () => {
        if(document.activeElement === $frame) {

          // Persistencia
          if((Date.now() / 1000 | 0) > adsProtectorSession.timestamp + self.expiration) {
            adsProtectorSession = self._sessionObj();
            self.current = adsProtectorSession.current;
          }
          adsProtectorSession.current = ++self.current;
          localStorage.setItem('adsProtectorSession',JSON.stringify(adsProtectorSession));

          console.log(`[click detected] ${self.current}`);
          setTimeout(window.focus,1);
          if( self.current >= self.limit ) self.protect();
        }
      });
    });
    },
  protect : function(){
    // Autor: https://es.stackoverflow.com/users/95211/dperezv-com
    console.log(`[Protegido] Sustituye por tu protección. Autor: https://es.stackoverflow.com/users/95211/dperezv-com`);
  },
  _sessionObj : () => ({timestamp :  Date.now() / 1000 | 0, current : 0}),
};

adsProtector.init();

jsfiddle.net/qsaw23co/

Expiration is defined in seconds.

Old version, no persistence

const adsProtector = {
  limit : 3,
  current : 0,
  query : '.ads > iframe',
  init : function(){
    const $ = (...args) => document.querySelectorAll(...args);
    let self = this;
    window.focus();
    self.$frames = $('.ads > iframe');
    self.$frames.forEach(($frame)=>{
      window.addEventListener('blur', () => {
        if(document.activeElement === $frame) {
          self.current++;
          console.log(`[click detected] ${self.current}`);
          setTimeout(window.focus,1);
          if( self.current >= self.limit ) self.protect();
        }
      });
    });
    },
  protect : function(){
    // Autor: https://es.stackoverflow.com/users/95211/dperezv-com
    console.log(`[Protegido] Sustituye por tu protección. Autor: https://es.stackoverflow.com/users/95211/dperezv-com`);
  }
};

adsProtector.init();

<div class="ads">
  <iframe class="iframe" src="https://es.wikipedia.org/wiki/Wikipedia:Portada" style="height:100px;width:100%"></iframe>
</div>

<div class="ads">
  <iframe class="iframe" src="https://es.wikipedia.org/wiki/Wikipedia:Portada" style="height:100px;width:100%"></iframe>
</div>

<div class="ads">
  <iframe class="iframe" src="https://es.wikipedia.org/wiki/Wikipedia:Portada" style="height:100px;width:100%"></iframe>
</div>