With a six man attack that I've got going, it's difficult to confirm which weapon is doing me more good, so I'm keeping both just to be safe. The former does more damage, but the latter is much quicker. However, when missing is taken into account, would the more damaging, albeit slower weapon make more sense? I know that this is a mundane topic, but the main page is littered with people having bug issues, so here's some lighter (or heavier) discussion.

All depends on your odds of hitting an opponent and the specific pluses and minuses of each weapon. Use some of that math you learned back when you were 13 years old and haven't used since then :)

(% chance to hit target) times (# of attacks per round) times (average damage per hit)

Compare this for Weapon 1 vs. Weapon 2 to determine average damage per round.

For example:
W1 = 0.3 times 3 times 3.5 = 3.15 damage per round.
W2 = 0.4 times 2 times 5.5 = 4.40 damage per round = Better choice.

Similar example:
W1 = 0.9 times 3 times 3.5 = 9.45 damage per round = Better choice.
W2 = 0.85 times 2 times 5.5 = 9.35 damage per round.

The light crossbow of speed should do more damage per round in most situations. But the heavy crossbow of accuracy needs less ammo and is therefore more comfortable to use.

Heavy Crossbow of Accuracy only has a +2 to damage. So unless you're fighting heavily armored foes that you have trouble hitting, you should use the Light Speedy one. If you have a decent THAC0, the extra attack will do you a lot more good than +4 to hit and +1 to damage. For bosses, though, you might want to switch back.

The best heavy crossbow (apart from Firetooth) is the Giant Hair Crossbow +3 from the Adventurer's Mart, which has +3 to hit and +5 to damage, which makes it a lot more damaging and effective than the Accuracy one. You need 15 strength to use it though. I generally prefer the Giant Hair to the Light of Speed simply because it doesn't chew through bolts as fast.