Why not have both. If the player makes the ships, the player can designate if it's an auto locking or manual turret. I can see auto lock turrets quite useful in a large ship that needs to defend from smaller ships. While the more manual turrets or guns can be had in smaller dog fighting type ships.
On top of that, even on the big ship you can still have both types.
So yeah, that shouldn't be an issue. have both types. Unless these devs are lazy and only does cut and paste programming, I would hope not.