I've been running around with semi auto pistols for the most part with reflex sights and a couple of headshots kills pretty much everything I've run into, even synths. Really? Because I have yet to find an enemy that takes less damage from a head shot than a hand shot. Although i find that shooting a lot of enemies in the head is a bad idea but arm is better as heads in power armour for example or synth armour are very well armoured, hands not so much. Well you do have sniper perks for vats i guess. I'm a better shot with a normal scope than what VATS gives me :\
I don't like the idea that you can miss in VATS unless your perception is perfect, and even then at an 90-95% of a chance to hit you can still miss, and with my luck (not the game Luck, just my personal luck) it misses more often than not. I don't actually snipe in VATS, I just use it to find the target.