Considering Caesar was working for him, he should have known all about the mechanics. It was everybody's expectation Ace would die; the whole event was about his execution, after all. So, it makes sense Flamingo would take an apple with him. It's another matter why he hasn't made a logia underling for himself, though. He had plenty of time. Surely he didn't foresee he might be able to, or rather might need to, use the fruit itself somehow against Luffy.
It'll be interesting to see what's going to happen to the fruit. I've always thought the Straw hats are kind of established as they are, and none of them would gain a new power like that. Luffy getting a double power might happen, since his Teach has two and he's probably the last boss, but who knows. Wouldn't that make Luffy too powerful before it's time for the final confrontations?