Just so you know, the core idea with some modifications could be neat, if not a little redundant, but my thought is if you wanted to see this useful and not completely OP. Make Plasma blades instead.
Here's the idea:
1) Plasma Blades could act just like the current weapon set. You have modules and computers.
2) The more modules connected the more damage it does. (the mechanics work just like current weapons. Example, if one shaft of 10 blocks is connected, it is one blade out the end. you can have more than one blade connected to one computer.)
3) It does NOT ignore shields, but does more damage than damage beams, and slightly less than damage pulse, except has very short range. (Example by default might have a 6 block sword that comes off the module.)
4) It will have no cool-down with no slave computers.
5) Uses more power than all weapons currently except damage pulse, but has no cool-down and uses power/sec while on. (AKA draining your power BIG TIME)
6) Using it acts as a toggle like an overdrive computer, but it drains TONs of power and toggles off if you run out of power.
7) It can have other weapon computers slaved to it and effects slaved to it.
8) They would add similar benefits as they do now. (Example, Damage beam slave adds longer sword range (up to a limit) and more damage, but also adds a cool-down to the weapon. Now when it toggles on it can only stay on for a short period of time, then it toggles off and has a cool-down until it can be toggled on again. )
9) Some bonuses would need to be different. For example Cannon computers slaved would not be able to reduce cool-down, so they instead will reduce damage and reduce power usage x2. All other slaves would add a cool-down toggle described like above.
10) Would be a minor addition to the game, but may add some versatility due to being toggle-able and being paired to other systems.
I think this is the only way something like this could be viable, but then again it will cause some fun balancing acts to implement as do all weapons in most games that are regularly changed. It would definitely need balancing after implementing, and that is the only true way anything of this nature can be implemented.
Also, I agree it is unfair for any weapon to bypass shields as it would be Over Powered, the problem currently is not as much giant-ism or titans as the game not having AI fleets implemented yet. Also, anyone will recognize this if they pay attention to how little the shields give you in defense along with the equations used to calculate recharging. It is currently balanced in the favor of small swarms.
The main thing not balanced in favor of small ships are the power reactors. They only get more efficient the bigger the dimensions are, and that is the only thing I think that "might" encourage giant-ism. Well that and being able to blow up half a planet with one missile barrage for fun.