So, missiles used to be able to glass-cannon a ship, but lo and behold, we got them nerfed (just like the countless list of other cool things we got in the game, and then had nerfed by threads like this)
So here's a thought. How about a Energy Weapon Cell Booster. Increases (maybe as much as doubles) the ROF of energy weapons for a short period per charge (or doubles the DPS in the case of beams). Drawback is obviously that it's going to overheat your weapons much faster, but it'll sap shields in a pinch. Lets face it, SCBs are useless once the target's shields are down, and the whole problem is that you can't deliver damage fast enough to counteract the effect of the SCB. This could also be a stealth-boost for armour reinforcement, as it'd become much more important if your opponent (possibly) has the (optional) ability to drain your shields in a snap.
Would this be balanced straight off the bat? Of course not. What about Ballistics, should there be a similar mod for them? Maybe, who knows, but hell, deal with that when it comes, because at least it's fixing something by adding to the game rather than taking away. Because lets face it, content in this regard is already a bit thin on deck. Missiles and mines are already useless and in dire need of fixing (more so than SCB's being OP, but again, Missiles used to be a fix for that. Funny what happens when you just nerf stuff eh?)