What I am proposing is that for weapons such as projectiles and missiles they have a clip or magazine of ammo, burn through that, then spend time reloading from a near infinite supply.
So for example the srm pods, would still have their normal ammo of 12, and their normal fire of 4 at a time, but when those twelve were gone the launcher would start a reloading bar to load a new dozen missiles, and that would take time.
by having a slow infinite reload this gives pauses in the output of fire that can be exploited by others to attack. Tying it to the ships endurance countdown would also be effective, when your ships effectiveness hits zero, the ammo well dries.
This slow reload would also make single missiles viable rather than a one off pray for a magic bullet.
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option 2 would be a new ship mod "arsenal bays". The mod would increase the missile ammo storage to 400% normal and reload time would be half, but ship health would be reduced by 65%. Using the aforementioned pod its ammo would be increased to 48, since missiles are the only ammo weapon left (mostly) it would give an option of staying power vs weakness.
could be graded to ship size ie 200%/300%/400%/500% ammo size. half reload time and ship health -65% would stay the same overall.