Crossbow bolts could pierce plate armor in short ranges, but the resulting damage wouldn't be enough to kill or even incapacitate the victim. Longbows couldn't pierce plate amor either.
Some say that most of the damage caused by arrow/bolts volleys were psychological. Most people wounded by arrows, even in pre-plate armor era, died by infection instead of direct damage by the arrows/bolts.
Currently, with vanilla raws, there is no decrease in lethality by applying any amount of armor. Even wooden bolts penetrate adamantine armor 100% of the time. In the vanilla testing in the great !!SCIENCE!! threads of versions past, with many thousands of marksdwarves firing many many thousands of bolts, a handful of deflections were recorded against armored targets. All of them were deflections off an eyeball, not deflections off armor. The only decrease in lethality observed was using metal bolts against armor of the same metal. In this case, rarely, the bolt would merge with the armor or something and turn it into a hammerblow instead of an bullet, letting it jam hands into wrists and so on. Notably upped the suppressive capability, but lowered the lethality(per shot, not overall. overall lethality was always 100%. Sometimes it took longer, though) by 10% or so.
Nerf your SHOOT_FORCE to 50 and your SHOOT_MAXVEL to 200. Steel turns aside wooden and bone bolts ~100% of the time, adamantine is bulletproof(but doesn't cover your throat and eyes etc) and copper/bronze armor is fairly good but not infallible protection against wood/bone but nearly useless against copper/iron/silver bolts. NB: your wooden bolts will be
slightly less effective against unarmored targets, but still deadly. It's up to you whether this counts as a nerf or not. On the one hand, armored opponents will be a little harder to murder and hunting may take two trips. On the other hand, now your adamantine hammerlords need fear nothing.