Oh yes!
Deer can definately hear the flight of an arrow. It doesn't matter what bow you shoot, an arrow will never travel anywhere near the speed of sound
I think I remember reading somewhere that if you shoot at a deer from 20 yards at 300 fps, the deer would hear the arrow and react while the arrow was between 4 and 5 yards away from it. Now i'm not saying that all deer will react, but loud arrow flight not only warns the dear, but with their supurb hearing, they can pretty much hear where the noise is coming from and which way to move. I know more than one hunter who has had deer duck an arrow.
My Opinion: Shoot something as quiet as possible and as accurate as possible and don't worry as much about speed, as long as the arrow is carrying enough kenetic energy to make a clean kill.