Perks that improve accuracy do work. May not seem noticeable, but you'll eventually start to see yourself getting "luckier" hits.
Perception doesn't affect your accuracy with weapons, all it does is show you where far-away enemies are, and gives you a higher "Sneak" attribute.
Are we sure about that though? Because when you're choosing your SPECIAL points at the beginning, it does say that Perception affects accuracy, which is why I put more points into it than I did in FO3. Now, it says nothing about accuracy if you look at it in your pip-boy or when adding through the Intense Training Perk, but I'm dead certain that it did say it affected accuracy when you're choosing at the very beginning of the game.