SO yeah a LOT of peoples have been tackling the ways of introducing weapons built in directly into the hull of ships and after playing a bit of Warzone 2100 (great freeware RTS btw) I think I figured out a way for this to work
The idea is actually fairly simple
The thing would be that the ship would have its built in weapon come in under the form of a simple "bullet emitter" coding wise that would be directly attached to the ship's sprite, pretty simple sounding, but I don't know how well it'll fare in actual practice...
Anywho that where I had an interresting idea
The hull based weapon would come in with no targetting systems
Simply because the weapon being directly stuck to the ship sprite it will be absolutely incapable of rotating otherwise you'd just use a freaking hardpoint
but here's the deal, thoses weapons would feature a special turret slot wich would have for sole role to field the targetting systems of thoses built in weapons, see it as a target painter
The ship itself will be capable of fielding thoses targetting devices to use the built in weapon in direct combat allowing the weapon to be fired automatically when a target get within its range
but its not all you could do !
you could use one of thoses target painter to tag a target far beyond the weaponship's sight for long range fire support hence giving a point in fielding frigates in late game fights as tag units
now everyone automatically thinks "HURR BUILT IN CANNONS DURR" but weaponships could also be built with massive missile racks all over like a Atlas modified to sport as many missile weapons its engine can hold spurting out enough missiles to overload a Capship's shield with enough time given, or a Paragon modified to feature a gigantic long range EMP weapon that could from across the map to disable entire ships unaware of the tag put on them...
My point is: we'd get a third type of fleet fieldable by peoples and it would be space artillery...