The problem is, maces tend to deal bruising damage over a larger area. This stacks up real quick, so you might get Bruise X 5 then the injured part explodes into gore, and this is an excellent way to deal with zombies. But against living opponents, armored or not, warhammers often deal disabling blows on the first strike. A broken leg makes you fall over, a broken arm makes you drop your weapon, a broken head is often an instakill. These blows may not pulp the body beyond reanimability, but they certainly reduce the ability of a living opponent to fight back. During the five or so bruising strikes a mace is likely to get before doing crippling damage, the enemy can be counterattacking.
I mean, maces aren't bad. I am fond of them, and often use them, if I have spare recruits with the skill, but they tend to get fewer kills than my hammerdwarves, and seem to be more vulnerable since they leave their opponents in fighting condition for longer. Still, legendary macedwarves with full kit will tear through goblins like nobodies business. But hammers are better.
EDIT: In my observation, legendary macedwarves have fair odds of getting "explodes into gore" reactions on the first strike, and break more bones. At this skill level, they are pretty brutal. However, for lesser skilled dwarves maces seem to do a lot of bruising, while warhammers work well even at lower skill levels.