Drakes are a temporary event so not much of an issue.

In case of bats, you could keep a portion of the herd in a sheltered area. Think of them as if being in labor or something.

Personally I think breeding is pointless not because of the animals being vulnerable, but because, other than chickens, you can get all the food and materials simply by hunting them in the wild. Having an army of guard dogs might be appealing to some but it sure isn't for me. :)

You don't have to raise animals if you find it overtly complicated. It would be silly if it was Minecraft-level easy. Seen enough games with that already.