To be fair, early on, it seems 2ndary weapons were designed for missles, you know, with the whole no range bonuses thing, but then it got co-opted too early and has been playing catchup for ordnance ever since.
I'd rewrite the ordnance from the gound up, an make the 2ndary gun weapons including PWT's work with ranges.
Ordnance would be thing apart from 2ndary weapons that were not subject to losing target locks and there would be a load out that matched the ship, though still costed points.
There would be a lot of balance issues of course, but it would make more sense.