You seem to make a mistake of thinking that games are a simulation of reality. They are not, and especially 5e is not. And even so they are there is so much systemic abstraction going on, that arguining about individual weapon damage stats without taking into account other systems can be counted as taking things out of context. You might as well argue why we get better by leveling up, and not by spending time practising the skill with an instructor.
I am not versed well enough in D&D to give exact balancing insight. Except for no1, though my knowledge is still limited.
Crossbows should have "loading" property. If I understand it correctly one can't use Crossbow with multiattack (you will still get single attack per attack action) So crossbows do a bit more damage, and can be favoured by characters who don't specialise in melee and don't rely on multiattack for their damage. Characters who do specialise in range combat, will be better of using a bow as it will grand them more attacks per-round.
As of now in BG3 crossbows don't have "loading" property (I think, I didn't test it in recent patch) so they very well be just a better option - if so it's on Larian. Maybe they will implement "loading" property for 1.0, now when multiattack became a real thing.
5. Why does a greataxe 1d12, but a halberd (which is essentially a long and heavy greataxe) does 1d10? Because of balance as the halberd has more reach?
That would be my guess. At least in BG1&2 one could reach with halibert from behind a tank, and attack enemy without yourself getting in attack range.
Balancing is a good thing. If one has a variety of weapons, there should be a reason for those weapons existance, and they ideally should be sidegrades. Trading damage for engagement reach seems like a very valid design for me. D&D 5e is meant to be straightforward system to understand (and is designed for table-top so it can't be too complex) so there is limited amount of parameters one can design weapons with.
There are only few parameters one can use to differentiate weapons:
damage, range, proficency, special rules like "loading". In case of BG3 unique weapon attacks. I think that's it. If you think there are other parameters that could make weapons more interesting I would love to hear them. Armor piercing could be interesting (like in PoE1&2), but for that we would need to get rid of AC and create something more granual.
