Well, since you didn't specify a camera, I'm assuming one of the Owls. With the 3 different Owls, having the AF sensors exposed does not seem to make much difference. Other camera types may be different - so it's best to test first if using a different model. On the flash light level sensor, might as well not bother with a hole since it's best to use 'fill-flash' anyway.
I always cut the extra holes for the AF sensors, even if the pics don't show much difference. Hate to lose that one in a million pic because the cam didn't focus right (only got around 990,000+ pics to go and I'm bound to have at least ONE worthwhile picture