Jason_the_Iguana: Still, there are other such undocumented features, like Kundane's Shortsword (I think) giving +1 attack.
Hickory: Kundane's sword is meant to have +1 to attack. It is called 'Sword of Quickness'. The usual way that items get incorrect, or 'undocumented', features is when they are copied and edited from another template. In this case though, there is not another single shortsword with +1 to attacks per round. The only other sword that does so is a scimitar (Belm +2). In both cases, this is intended.
Yeah, it's intended. But it's still undocumented or at the very least poorly documented. The description for Belm and the Scarlet Ninja-To say that they give an extra attack. Great. Kundane only says "Special: no speedfactor" or something like that. Which isn't helpful at all, especially since there are other weapons with 0 speedfactor. (For example, a plain dagger + 2) You need to know, from practice or external sources, that in this particular case the zero speedfactor translates to an additional attack.
My point is that weapons in BG aren't always very clearly described. But you're right that most of these are probably indeed working as intended, it's just the descriptions that aren't clear.
Hickory: Yes, a warehammer is better than a mace generally, because it is faster -- maces are very slow. Your 2D4 is better than 1D6, even if they were the same weapon: 1-6 damage vs 2-8 damage. When comparing weapons, speed should always be a major consideration. For example, in BG2 the Tuigan bow is only +1, but because it grants 3 attacks per round it does more statistical damage than bows of much greater power.
This, however, is not true. Maces and warhammers give exactly the same number of attacks per round. Speed Factor, except in the case of Kundane, does NOT affect your number of attacks per round. It just affects how quickly your first attack will come. (the Tuigan Bow does give an extra attack, but that's a unique property of this weapon, like Kundane and Belm we mentioned above. It doesn't have anything to do with its speed factor.)
So, suppose you have 1 attack per round. The engine may show you attacking 3 times, but only 1 of those is actually rolled. In this example, a guy with a dagger would make a real attack, then the engine would show 2 fake attacks. A guy with a warhammer might make a fake attack first, then a real attack, then another fake attack. The guy with the mace might make 2 fake attacks first, then a real attack.
The dagger guy has the advantage. He can more easily hit a moving target, for example, who might not be in range long enough for the engine to roll the fake attacks first. This is especially handy for thieves trying to backstab. But in the long run, all three guys attack 1 time every 6 seconds.
As for damage: Warhammers inflict 1D4 + 1, (i.e. between 2 and 5 points) maces 1D6 + 1. (i.e. between 2 and 7 points) So on average, maces inflict 1 point more damage. (Unless the enhanced edition changed this, warhammers do not inflict 2D4 damage. Morning Stars, however, do.) In practice, I'd say that neither this 1 point of damage nor the speed factor difference is very important, especially once you get magic weapons which have lower speed factors anyway. The more important factor is finding a cool magic version of your weapon.
Minor spoiler: both in BG1 and BG2, there are better warhammers than there are maces, i.m.o. But there's also a magic flail in BG2 that may actually be best of all.