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:

http://www.naturescapes.net/042004/do0404.htm

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.

www.heatherforcier.com

Heather Forcier
Burlington, VT