For the archmage warhammer I have 50-62 melee damage, 15-18 magic damage, with a bonus +26 magic damage with the full set equipped. Perhaps Larian figured anything that got close enough for melee combat was either weak or resistant to magic, so could use some extra conventional damage. Maybe they figured a high intelligence character would end up with a more balanced damage that way.
If you are duel wielding, put the warhammer in your off hand, or use a different weapon (there is not a huge drop in set bonuses with one less piece: 1 less armour rating, or 2 less HP/MP).
