If your ship moves sluggishly, has poor shields, and turns like a capship with one engine shot out because of your guns.... yeah, it's overpowered. The reasons that fighter loadouts get balanced are probably because a) the fighter can't be TOO expensive to produce, given its mission, b) the capacitors need to be able to support the guns, and c) the guns should support the mission.
In other words, sticking a pair of plasma cannons and tachyon guns on a scout craft, while giving it a powerful loadout, would probably not be a good idea since I doubt it has the armor to make use of guns like that, much less the space or gun-capacitors required. Granted, the speed would make the guns useful... but the other disadvantages outweigh those advantages, and a pair of long-range guns combined with medium-range ones (ions and mass drivers) would probably do better in that situation, though you might also want to keep the guns light to ensure the pilot doesn't try to duke it out in a dogfight with heavy fighters.
Secondary guns are, IMO, overrated - they did cool things (the stormfires especially), but I'd rather just stick with six guns on a heavy fighter or bomber.