I have a question - in the 2-hand tree, there is a perk (which can be upgraded 2 additional times) to give 25% armor bypass to warhammer attacks, for a total of up to 75% armor bypass. Does that perk also apply to enemies which don't wear armor in the normal sense, but have 'natural' armor (I can't think of any at the moment, but I'm guessing some critters, atronachs, draugr, etc might have some inherent resists)? Does it apply to magical 'armor' from the Alteration tree?

I'm curious to see of it goes through a ward or a spell like oak flesh/ skin to.

Assuming natural armor is a numerical value and the mace perk bypasses a percentage of the numerical value of your armor, then yes.

I haven't used maces or the perk in my playthroughs though, so I'll defer to dragonkillers that use them if they hit a great deal harder than with the other weapon types when perk'd.