Pokemon are eaten. It is fact:
Farfetch'd a l'Orange
Magikarp fillets (though said to be very tough)
Slowpoke Tail (which grows back, so they farm them)
Taurus Steak (it is mentioned)
Those are just the few I remember off the top of my head. As for farming them? Pokemon gain strength by battling. If they don't battle, they'll never learn new moves, so it'd be quite easy.
The question about real animals being in the show is quite simple: the show is a poor representation of the manga/games. In those, Pokemon do completely replace animals. There are a few places where animals are seen in Season 1, but as the seasons progress they start to make less and less continuity mistakes.
Farfetch'd a l'Orange
Magikarp fillets (though said to be very tough)
Slowpoke Tail (which grows back, so they farm them)
Taurus Steak (it is mentioned)
Those are just the few I remember off the top of my head. As for farming them? Pokemon gain strength by battling. If they don't battle, they'll never learn new moves, so it'd be quite easy.
The question about real animals being in the show is quite simple: the show is a poor representation of the manga/games. In those, Pokemon do completely replace animals. There are a few places where animals are seen in Season 1, but as the seasons progress they start to make less and less continuity mistakes.