Blackbeard's darkness only works when he's touching you. And he specifically says it doesn't negate attacks, it absorbs them and he takes the damage. Why would it work on Ace's fireballs? Even if he grabs Ace, the fireballs just become normal fire, they don't vanish.
But I haven't seen a single instance of Haki being used to negate a Devil's fruit power other than someone's invulnerability. So I find it more likely that Haki can penetrate invulnerability rather than negate Fruit powers. I don't see anyone using Haki to turn a Zoan back into a human or to negate any other Paramecia powers. It's only allowed attack that the target should have been immune to work.