Most (practically all) aircraft do not have bullet-proof windshields (including military), for starters, and secondly a several pound meat ball travelling at closing speeds anywhere between 60kts (GA) to 200+ kts (jets/airliners/mil) is going to do a number on the aircraft regardless if it incapacitated the pilot.

Doubly-so if it's a several pound metal ball...

You don't want to hit anything in an aircraft, ever.

Actually, I'd say the most vulnerable part for a strike in a single engine craft is the engine, which sits ahead of the cabin. At low altitudes there's precious little time to correct for any sort of engine failure.