I've read in multiple different places that using flash isn't such a good idea while taking pictures of animals as it hurts their eyes and can even cause seizures in rare cases, I would imagine it would only be worse for nocturnal animals whose eyes are very sensitive to light. Maybe you could just try to capture them in the brightest possible ambient light instead? I never use flash in my pics (just in case) and most come out just fine. Better safe than sorry, just my two copper.
I would like to see reliable documentation of this. I've heard flash during the *development* of the eye is not good (such as through the thin eyelids of a young animal), but not that it's bad on a fully functioning, normal eye. Eyes are made to receive light, and I don't see any reason at all that flash shouldn't be used other than the "stress factor". Of course, if I saw anything with actual research done I'd be willing to change my mind. JMO.
Aside from that, I take pretty much all my pictures except for ones outside with flash, otherwise you have to have a crazy good camera to get clear pictures in the lower light. This includes people, animals, even very young baby mice/rats (pinkies) with black, ruby, pink, and red eyes. None have had any ill effects that I have seen. Someone of course will rip on me for saying "your good experience is nothing compared to something negative that happened one time" but again, JMO.