I'm probably in the minority, but I think a simplified, consistent hull bonus system seems like the best way to implement armor and armor piercing.
Pick an ammo type to be associated with armor pen. Pick an armor type, or possibly types, to be associated with having lots of armor. Give that ammo type a consistent multiplier bonus against things with armor. IE, declare that energy bombs are good at hitting big heavy targets, and give everything with energy bombs a consistent, high bonus against heavy. Make everything that's supposed to have heavy armor use that hull type. If necessary, add AP missiles as an ammo type and ultraheavy as a hull type, with AP missiles giving some bonus vs heavy but a huge bonus vs ultraheavy.
Then just get rid of the entire concept of flat damage reduction, aka the current armor system. Stick to ONE representation for armor and armor pen. If you must have flat damage reduction, give it to ONE unit as their special schtick.
Currently armor either 1) acts as flat reduction, which interacts in really complicated ways with reload time and shot size, is hard to eyeball, and is prone to having lots of relatively subtle effects, or 2) the target has so much armor that you hit the 80% damage reduction cap, which is exactly equivalent to giving AP units an extra 5x multiplier. It's also not consistent what has armor; does everything with a heavy hull have armor? does everything with an ultra-heavy hull have MORE armor? I don't think so... if it was purely hull type based, then that WOULD be consistent.
Or, I guess you could have an 'armored' tag and an 'armor piercing' tag that acts as an extra multiplier, possibly stacking with whatever other tags are around, but I suspect that could rapidly get even more complicated than the hull bonus system if you have a lot of tags.