Sealed away from the Heartless. They sort of collect in the Realm Between, and with a bit of prompting can come together to form a false Kingdom Hearts. But it takes a lot of them to do that; not sure of the exact number, but it's gotta be in the hundreds of thousands at least. Maybe millions.

And the fact that someone managed to do it, and it didn't seem to even put a dent in the overall Heartless population of the worlds should tell you how much of a problem they are back home, even after all Sora and his friends have done.