The original proposed solution of limiting max armor is not actually a problem.
As I noticed in my aborted AAR, those armor balls are way too expensive.
Even with 4 layers, They would last a decent amount of time, so just build several.
Alternatively, with more cost, but significantly less build time, 2-3 layers of armor and a few dozen CIWS do the job as well, and you don't even have to repair it.
Armored Cluster-Missiles do the job as well.
While we're at it, in the same way missiles are limited to 1 MSP+ (I still think there should be a tech line to reduce size), in the same vein it's possible to build a multi-stage missile, where each stage is above 1 MSP, but only the last one is really a useful missile, all others are just 0.1 MSP+filler.
The real solution to all those problems would be an AI change, like stopping NPRs from always shooting at the biggest target, which has proven to never be the right choice, and prioritizing big missiles over small ones, unless known, in which case WH size should do.
No matter what is done, someone will always find a way to fool NPRs to fire at useless junk.
Unless theres more spoilers.^^