I subscribe to the theory that yes, they do eat Pokémon and whatnot because they're the Pokéverse's equivilant to our animals. I mean, Pokémon eat other Pokémon (the flavor text on one of the older Pidgeotto cards confirms this). Why couldn't the humans eat Pokémon, too?
I also go by the *SPECIAL manga rather the anime, too... So that could be it.