Okay.... the difference is because of different shields are used for capships and for fighters (at least since times of WC2, while WC1 the phase shields were not invented, so the weak "bubble" shields were also used for capships, same technology as fighters, just bigger and with more energy in it, so a little bit stronger).
Capships etc. use PHASE SHIELDS. Phase shields cannot be penetrated by anything, regardless if it comes from the outside or the inside. So the turrets can't be shielded, otherwise they could not shoot.
Fighters etc. use "BUBBLE" SHIELDS, which can be penetrated by anything that comes from inside, but blocks things from the outside (or tries to block it).
Another problem is fighters launching. Obviously you cannot land on a ship, while it's in combat, because the shields have to be inactivated for a brief second or two (long enough for the ship to take serious damage). In WC1 it's no problem to launch fighters while you're under attack, because you only have the bubble shields. But in the never versions it has to be something else. First possibility: The launch bay isn't shielded by phase shields, but only by the energy field which keeps the athmosphere in, but can be penetrated by solid objects that come out of the hangar, but blocks everything, just like the bubble shields (perhaps it's only a slight variation of the technology), that comes from the outside. The other possibility is, that the fighter's (bubble-)shields are adjusted to the same frequency as the capship's (phase-)shields to allow the fighter to pass the PHASE shield.
The torpedoes can penetrate the phase-shields, because it analyzes the shield frequency and has some sort of own energy field around it, which is adjusted to the phase-shield's frequency.
Other missiles just explode on the shield so it loses energy. Laser Cannons and such things are to weak to do serious "damage" to the PHASE shields.
Obviously it is not possible to set the guns to the same frequency as the shields, because the enemy hit by it could find out the frequency and/or it just doesn't work just because the frequency range of shields and guns are too different.
I hope this explains the things. This is, in fact, how I would explain it and how I think about it. (I explained it my little brother that way!)