Using Number.prototype is SLOW, because each time you use the prototype method your number is wrapped in an Object. Instead of this:

Number.prototype.mod = function(n) {
  return ((this % n) + n) % n;
}

Use:

function mod(n, m) {
  return ((n % m) + m) % m;
}

See: https://jsperf.app/negative-modulo/2

~97% faster than using prototype. If performance is of importance to you of course..

Most languages which inherit from C will return a negative result if the first operand of a modulo operation is negative and the second is positive. I'm not sure why this decision was made originally. Probably closest to what processors at that time did in assembly. In any case, since then the answer to “why” is most likely “because that's what programmers who know C expect”.

The MDC Reference contains a pointer to a proposal to introduce a proper mod operator. But even that would keep the existing % operator (which they call “remainder” to better distinguish between them) and introduce a new infix word notation a mod b. The proposal dates from 2011, and I know no more recent developments in this direction.