Its definelty a loose end. It can't be different mom's, as then all 3 generation would have to have the same mother to get the Monkey D. name! Plus, its the father's name which carries on as the family name anyway.

If I had to make a guess, I'm thinking there might have been a bust up between Ace and his family, and he left in such a State that he just picked a new name. Or something like he wasn't happy with his father Dragon's or his grandfather Garp's line of work and he didn't want to be associated with them.