I must have been too late for the missile regen/reloading topic, and i have only read the first 60 pages so my following idea/suggestion might have been proposed already:
First, regen mechanism:
I think it's better to design some ammo fabricator hull modules which requires high OP so that normally they can be only installed onto cruiser/capital ships (some destroyers might worth a try if they are not lacking OP elsewhere too much). I don't know if it's easy to implement different types of ammo fabricator, like for bullets/shells, or for missiles/torps so that we can give different costs to them so that even frigates/destroyers can install one for bullets/shells.
Second, about reloading:
Why don't we simply have two variants of missile launcher for Pilum, Salamander, Reaper, etc? One variant that has much lower OP is simply an external rack that cannot be reloaded from in-hull weapon bay during a battle (it might have its own ammo reserve though). Another type has much higher OP for the reloader devices and a weapon bay for more ammo.
The purpose is not to pursue realism, but we can get some good references from reality: e.g. on modern missile frigates/destroyers, we have twin-arm launcher which can launch two missiles quickly, but takes ten seconds or more to reload from the weapon bay which is located under the turret.
So making player have their choices depending on their play style: either long solo battle which requires more endurance or a quick strong assault to kill everything on the field, might be a good solution.
e.g.
Reaper Torp Rack: 1 rack, 1 torp. 1 OP.
Reaper Torp Tube: 1 tube, total 4 torps. 6 OP. // OP/torp increased due to reloader devices/storage.
Typhoon Torp Pack: 2 tube, total 4 torps, 8 OP. // OP increased compared to the Reaper Torp Tube due to complex launching device which brings better salvo capability.
Typhoon Torp Launcher: 2 tubes, total 8 torps, 15 OP.
Cyclone Torp Pack: 4 tubes, total 8 torps, 18 OP. // OP increased compared to the Typhoon Torp Launcher due to even more complex launcing device which brings even better salvo capability.
Cyclone Torp Launcher: 4 tubes, total 16 torps, 26 OP. // OP/torp slightly decreased because some devices' OP costs are not linearly increased when torp amount get doubled. plus, such high OP device will be cautiously chosen by player so a small discount might be needed.
Well the exact numbers can be tweaked, but the overall idea is like this.