The point of this thread is really not to argue that crossbow bolts are overpowered or not, it is merely to study the effect of armor at stopping bolts. It was actually somewhat a surprise (at least to me) that the answer is that armor does absolutely nothing against metal bolts.
In my personal opinion, vanilla crossbows are relatively well balanced in fort mode, as on average the fact that armor does nothing is balanced out by shields/dodging being super effective against them. I played a fort through to see what impact my suggested mods of more realistc bolt masses/energies were, and found that they had almost no impact at all because my (uber skilled) dwarves almost never got hit by bolts. Furthermore, the amount of damage done by the less massive bolts did not decrease noticeably. My marksdwarves were still extremely effective against goblins, even though their shots were occasionally deflected by armor. Overall, the amount of deflections you'd expect realistic armor to produce is low enough that it simply isn't noticeable in fort mode.
That being said, it is VERY noticeable in adventure mode. Things don't "average out" when players realize this is the tenth time they got shot in the head by a copper bolt, and their iron helm did nothing...again. Also, in adventure mode archers tend to make a lot of shots "from behind" and such, so dodging/shields and such are less effective.
Bottom line - I think crossbow bolts can be relatively simply modded to allow them to work very well both in fort mode and adventure mode. For the quick and dirty way, try setting [SHOOT_MAXVEL:833] in [ITEM_WEAPON:ITEM_WEAPON_CROSSBOW] and [ITEM_WEAPON:ITEM_WEAPON_BOW], and [SIZE:11] for [ITEM_AMMO:ITEM_AMMO_BOLTS] and [ITEM_AMMO:ITEM_AMMO_ARROWS] (I also posted a mod somewhere in this thread that uses custom materials to give all bolts the same mass, but this kind of makes a mess in fort mode). If you can see any difference in fort mode, I'd really like to know about it, and you will almost certainly notice a difference in adventure mode. In particular, for reasons I don't quite understand, helms seem to be made particularly effective, so this change should drastically reduce the number of one-shot deaths from archers.