FS2 capships suck- anything you, flying a vessel maybe a thousanth the size, could take on and beat easily just plain sucks.The Aeolus and maybe the Lilith were the only capships in the game that even presented a challenge. Ravana came close, I got pegged by an anti-fighter beam more than once, but it had too many weak points in the end.
The real problem isn't really turrets- in the original game, capital vessels were down right scary to face off against, and you didn't want to be doing a bomber run. Particularly in an interceptor (which is actually the ideal way to do it now, pretty much). The problem is, as with so many things in the game, they were balanced for FS1. I recall in original FreeSpace, before the shields came around, taking on a friggin' Mentu was a tricky proposition. Shields upped the disposable ship HPs almost tenfold, especially counting their regeneration and localization properties, and fighter weapons were boosted accordingly so it wouldn't take an hour to down a Dragon, but since capships don't get shields they stayed the same.
Forty capship guns ain't so bad if any one of 'em can do serious damage to you with one hit. Forty guns sucks if they're at best about the same as the weakest fighter gun.