This is a false problem, I just presented the fact that you cant do fuck all about all that; you can speak about morale or realism or whatever, its down to whether you do it or not.
The real problem is that we are still playing a game, even knowing about all those problems, and we try to get around it in whatever way we can.
Then, about the weapon racks themselves... 5 is an astoundingly low limit, you can build them in less than a minute if you're fast enough... During the preparation phase! If I was really playing just to win, I would do that in every defensive battles I got on.
5 weapons racks in one castle wouldnt be over-stretching either, there is more than 1 or 2 archers spot in a siege. Also, you want to have some weapons racks already built in case the first are destroyed. So not only it is "allowed", but it is also completely worthy from the strategical point of view (without talking about the "denying" items limit). So trying to put an artificial limit of 2 or 3 per side would be accepting the fact that this part of strategus is fine, instead of willing this situation to be fixed.