Well, remember when Sora became a heartless in KH1? I think these particular Heartless do no have particular owners, but are just made from the darkness in peoples' hearts, as the game explains. They are simply meant to serve as enemies. Now why do you not see many people in Traverse Town? Really, Square just wouldn't bother making tons of people. But perhaps they would have more if only...maybe all those people turned into Heartlesses, yet the only ones who didn't were stronger than them, like Leon, Yuffie, and some of the miscellaneous talking NPCs.
OK, back on topic. These are not supposed to have specific owners, and remember that Maleficent was using Ansem's machine to manufacture Heartless. So perhaps these secret bosses and other enemies are no more than manufactured ones. And if not, maybe the secret bosses flooded out of the Keyhole in Hollow Bastion. Remember how right when you sealed teh keyhole and ran away to Traverse Town, and went to Neverland or Agrabah, you could fight them? I think they might've come out of the Keyhole Of Darkness. What do you think?
Feel free to discuss.:thumbsup: