Actually there's an explanation as to why weapons would take up both slot types. It's simply because at that time, ship resources were limited to having four weapon slots, but a player could add in more, thus giving them a far more tactical advantage over their AI ship counterparts. So by using up both slot types, it would balance the game a bit between players and AI ships.
Also, I believe the AI at the time couldn't properly handle firing turreted and fixed primary weapons at the same time. The option to install both guns and turrets up to their respective slot limits permits the player to outgun any NPC ship equivalent to their own, which is hardly healthy for gameplay balance. The gun/turret slot limitations, as implemented in EV Override, ensured that the player's ship was kept nearer to the level of the player's foes. Incidentally, this also gave incentive to invest in ammo-dependent secondary weapons that might have otherwise been overlooked for that all-important decisive edge in relative firepower.
Incidentally, while changes to the game engine and AI routines in EV Nova rendered it technically unnecessary for turrets to also occupy fixed gun slots, I can't help but speculate as to how gameplay balance might have been affected if that particular feature, maligned as it is, was left in.