Not sure about a cooldown; one issue there is that if it's not too long, then it could get pretty insane, with tons of missile spam. And I'm not a fan of super-long cooldowns.
Would being able to fire off the entire missile load every 30 seconds or so be OP? Kind of seems like it would, doesn't it? Might just have to try it and see.
Yes, that seems OP. 90 or 120 seconds would seem more appropriate. Why are you not a fan of that? Seems simplest.
Another idea would be that the system reloads only one missile rack at the time. Say always the one with the lowest remaining ammo percentage, and if that's identical the bigger sized weapon first. The rack is out of order until reloaded, which takes something like 15/20/30 seconds, depending on size (saying 15s since small racks are disproportionately dangerous because of their alpha strike capability). Also, continuous flux costs when the system is active.
That way you
could pull back and completely reload everything, but that would take two minutes. You can also stay in the fight with an always slightly reduced missile capacity and reduced effective flux dissipation. Seems like an interesting tactical choice. For the AI that's something were officer personality could come into play, I guess.
I made a similar ship system in Seeker for the Clipper: it's a toggle system that reload the missiles progressively (like 2% of the max ammo per second) and lock every weapons in the meantime. Of course that's logical in this case because all it's weapons are missiles, even the PD. Anyway it work pretty well and don't seems overpowered.
I liked that system, but IIRC the missiles were built in? I'd imagine it would be difficult to transfer to a ship with variable missiles, since those have widely varying ammo counts/relevance that can't be easily abstracted. It would probably end up strongly favoring one certain type of missile. Think e.g. about single shot reapers, when would they be reloaded, early or late after system activation?
@ Soldier: That sounds like fun, I'm gonna try a blockade too
How many supplies did you pack?