It doesn't cause them any harm as it doesn't cause us, but if they're under a hide in the dark you may not want to be snapping pictures with a flash, I'm sure you wouldn't want that as well. Otherwise no issues
Keep the area fairly bright before flash, nocturnal animals in the wild are often killed by 'trap' cameras with a regular flashes (not ir versions) I use studio gear (dynalite) to shoot mine some don't care others don't think to much of it just make sure it isn't way dark, that is all.