The impact of flash on the visual system of wildlife is a good question, and
one I have heard discussed for years with not much for information available
on the subject. In my role as Editor in Chief at www.NatureScapes.Net (an
online resource for nature photographers), we were finally able to get an
informed article written by a veterinary ophthalmologist and an
ophthalmologist called "Flash Photography and the Visual System of Birds and
Animals." You can find it at the following link:
Hope this helps address some of your concerns regarding use of flash.
Regarding the reaction of subjects, it can vary - some will leave with the first
instance of flash, others will take notice of the first flash but ignore
subsequent use. For instance, raptors are incredibly cautious (flash or not),
whereas shorebirds can be pretty tolerant of photographers, their clicking
shutters and flash units. In many years of bird photography, I have never
seen (to my recollection) a bird attack a flash unit. If they react, it tends to
be in the opposite direction.