If you mean bats have ruined or at least made it more difficult to have simply fenced breeding operations I would say they have not ruined the option, just made a bit riskier.

So it is possible to keep most of your animals in simply fenced pens (off-site for example) while keeping your breeding animals a bit more protected.

The issue really seems to be there are no player made defenses available to help deter 'flying' raids from things like bats and drakes and who knows what in the future like we currently have for land raids (like spike walls).

Maybe we need something to slow flyers down so players have a bit more time to draw them off?