This is an awesome idea. I think it should be doable with FLHook magic.
Perhaps use the damage multipliers that are available on weapons against shields and convert them for use here?
This would give good RP material for capital class ships for specific tasks and would also help in giving some capital ships specific support roles for aid in battle or patrols.
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Also, these kinda reminds me of the subsystems on capships in "Homeworld II".