Using Number#valueOf:

The valueOf() method returns the wrapped primitive value of a Number object.

Number.prototype.inList = function (list) {
  return list.includes(this.valueOf());
}

let value = 0;
console.log(value.inList([0,1]));

This happens in non strict mode, where compatibility requires that this is always an object, not a primitive. So in your case this is an instance of the Number constructor, and of course that object does not occur in your list.

In strict mode your code works, as this will be the primitive value (number)

Number.prototype.inList = function (list) {
  "use strict";
  return list.includes(this);
}

let value = 0;

let find1 = value.inList([0,1]);
let find2 = [0,1].includes(value);

console.log("find1", find1); // true
console.log("find2", find2); // true

Here the strict mode is only effective on the function -- and this is enough for this issue. If your script has no "legacy dependencies", you should better set it globally.