Yes and no.
I think that if the weapons weren't affected by skills the way they were, they'd certainly be excellently balanced. I'm just not that much of a fan of my Skill percentage determining the damage output of my weapon; that should be up to its condition and the very nature of the weapon itself. At the same time, I LOVE that you were penalized for using some weapons without enough ST or the related Skills. Requiring 6 ST and 75 Guns for a Sniper Rifle to function optimally, while still being able to USE it, albeit with difficulty aiming (which a skilled enough player- such as myself -could compensate for ^_~) was a great system.
Some of the weapons themselves were ridiculous (in the sense that they just DIDN'T compare at all to other weapons, like 9mm Pistols, Varmint Rifles, etc) but as a whole, I think the weapon balance was pretty solid. The very fact that I still read other players' testimonies of playing the game with completely different weapons than I'd ever think to try is a testament to their balance. =)
So yeah, they're pretty balanced overall. Not perfect, by any stretch, but for end-game gear, the variety is really remarkable and well-balanced.