i've noticed the same thing. the animals seem to be less available over time the longer you play, but if you log out and back in, there is a noticeable increase in animals again. It's been like that for at least the last 3 alphas.
they still spawn for me if i keep the game up, but for whatever reason, there is an increase on restart or re-logins. maybe the animals are mostly chickens and rabbit the longer the game runs and it's just harder to see.
I also remember that they said animals would stop spawning in an area for a while after you killed them. That was 1 or 2 alphas back at least, so i don't know if that is still in place. Obviously, logging out and back in cleared that, including now.