I've gotten some 50,000 pictures with digital game cameras over the last couple of years and I haven't seen any real evidence that the flash spooks deer.

If it still concerns you the better cameras can be switched to operate in the daytime only, but you know that deer move a lot at night and you will miss a lot of deer movement.

I've tested two cameras with IR and I wouldn't buy one if it were the only camera I were going to own.