1) 3As were allowed in the sp before there were "more than 2 or 3 landing them in competition", why shouldn't quads be?
The difference is that triple axels are triple jumps. The SP requirements since the mid-1970s have allowed triple jumps in the jump combination, since before any men had landed 3A in the freeskate. Which triple jump was up to the skater. It took until the mid-1980s for men to try 3A in their SP jump combinations, and by the early 1990s there were two women doing the same.
The wording had always allowed for them in the combo, but the skill levels of the skaters took a while to catch up.
But it was a lot longer before triple-triple combinations or solo triples were allowed in SPs (even for men, because of the required double jumps), let alone triple axels as the solo axel or quads as solo jump or in combo.
2) Why should the rule be determined at all by how many athletes can do a certain thing?
In the short program, because short programs were designed to compare apples to apples and to ensure that all skaters could demonstrate certain specific skills that everyone at that level should be able to do. Short programs by design have never been about pushing envelopes.
Maybe the short program has outlived that purpose and needs to be rethought.
In the freeskate, everything men are allowed to do women are allowed also. Especially now that men are no longer allowed an 8th jumping pass. And anything that fits the much broader freeskate rules is allowed even if no one has ever done it before.
But there are still some things that are not allowed in freeskates, or not rewarded by IJS and therefore not worth doing. I personally would much rather concentrate on ways to encourage unique skill development in freeskates.
No one tells Usain Bolt that he can't run a certain speed and have it count because he's the only one doing it. No one tells Simone Biles she can't do a triple-double in her floor routine because she's the only woman that can do it.
And no one tells female skaters that they can't do quads in their freeskates, or any other skill that meets the same rules that men and women are subject to.
But they do tell Usain Bolt that they won't give him medals for how fast he can run, say 163 meters, even if that would be the distance at which he could maximize his speed.
And they do tell Simone Biles that she can't compete on pommel horse, because it's not part of the women's gymnastics competition.
As far as I get it from your post, not a single element is forbidden in men’s SP,
There are lots of elements that are forbidden (or, as I'd prefer to put it, don't meet the requirements) in men's SPs.
As I mentioned in my previous post, quad-quad combinations have no place in a short program. Nor would a quad-Euler-triple combination or any other three-jump combination, or a triple axel or quad anything-triple axel sequence. Or one-foot axel-quad salchow combination -- both jumps in the SP combination must be at least double and one of them must be (at least) triple.
Same with the spin elements I mentioned in my previous post. Flying combination spin? Not allowed in the SP. Change-foot upright spin? No (as Jeremy Abbott once learned to his dismay after having failed to read the rules carefully enough). Any flying spin with change of foot? Nope. Any spin with more than one change of foot? Nyet.
All perfectly fine in freeskates, not according to requirements in SPs.
but a quad, that men are allowed to have in SP, is not allowed to the ladies.
And a solo layback with no change of foot is allowed in the ladies' SP but not allowed to the men. Or now, for that matter, a camel or sitspin with no change of foot.
If there's a man out there who can do a beautiful level 4 layback into Biellmann, he can save it for his freeskate, but it won't do him any good in the short program, aside from whichever of those positions/features he can work into his combination spin.