Simply put, Yangfan, I think your system is too complicated. Loyalty and such are something to consider, but I don't want to mix them with shipbuilding.
Subsystems are already accounted for with the recent system. The chart is set up in such a way that any current or new ship should be fairly easy to measure in both damage ratings and resource points.Writing ship designs is itself is a complex OOC task, and you really need to account for each subsystem to avoid abuse. Otherwise people will just cram hundreds of guns onto a hull and call it a "light escort".
Yes, their points are measured as Damage Rating multiplied by 10 multiplied by the total number of actual gun emplacements of that type. Sakura's a bad example in that one respect - I just counted all the pods as one system, since they're all generated in the same place as needed.Secondary Guns - does the figure change depending on the number of guns you have? The basic rules don't make it clear.