Not to mention death by Hypno or Drifloon. I know their dex entries just say your taken, but your never seen again.
I'm assuming that means death. either that or they are hosting one mess of a party. They must have a lot of free food...
It could be an in-universe equivalent to faeries stealing people to make into changelings:
http://en.wikipedia.org/wiki/Changeling
Basically, according to legend, faeries sometimes steal people (typically though not always children) to use for various reasons (pets, slaves, adopted children, for use in experiments, sex slaves, just to be jerks, etc). They may or may not leave a "fetch," or a copy (typically enchanted twigs or a fae child) as a replacement of the person they took. Occasionally, a faerie might get bored of their changeling and release it, but by that point, the changeling has been exposed to the faerie world long enough to cause several problems:
1) They're not entirely human anymore, and may have mutated or may have powers beyond his/her control either due to prolonged exposure to the faerie world or due to the faerie deciding to make cosmetic and functional alterations to their human.
2) The faerie world operates on an entirely different moral and logical system than the human world, and drives most people insane after a while, so some people become no longer able to function independently. They might not be able to understand or clearly discern the differences between worlds anymore.
3) Time passes differently. A person might have spent years in the faerie world but was only gone from the human world for minutes, or may have only been in the faerie world for a short time yet gone from the human world for decades. Or they could even go back in time.
4) Some find themselves drawn back into the hedge because the faerie world is now more familiar than the human world.
So there could be Pokemon out there with insane humans as pets and slaves and (not necessarily willing) lovers. And they could be modifying their humans to suit their tastes.
And this is one of the reasons why I won't be the least bit surprised if we start seeing Fairy types with really horrifying PokeDex entries.
And this totally gives me a new story idea.... I was already going to have a hedge-like horror town, but I might have to up the ante or do a much darker game on the side....