The military slots should have replaced ordinary slots, but that could not be done because FD never allowed you to store filled cargo in a station (which would not have worked anyway if there were no "Outfitting" at the station dock, so they would have had to add that to every dock too). So the only option here is to undo the imbalance of HRPs.
REALLY SIMPLE METHOD:
They become a "second hull". When your ship takes damage, 50% (as an example) goes to the ship hull, and 50% goes to the HRPs installed. The % taken becomes a maximum multiplier. Engineering to higher levels would cause a lower durability (when durability goes to zero, it cannot take on any damage, so 100% goes to hull now), and engineering resistances would affect THE HRP ONLY. If you had an unbalanced 100% resist all, it would add nothing more than the HRP doesn't wear out in battle. Your hull still takes damage. At 50% damage sharing, the HRPs can only add up to double, and then only if the HRPs have as many, or more, hit points as the ships' hull.
I think it should be possible to make a HRP that intercepts less damage but DOES add to the corrosion resistance: it would be a honeycomb filled with neutralising agents, it breaks when hit (so intercept SOME damage) so as to release the counteracting agent to the corrosion agent on the hull itself.
I would want to see the Reinforced/Military/etc hulls reduced in mass, AT LEAST HALF, maybe a quarter, to make them useful for more than combat oriented builds, and more than merely Heavy Duty Lightweight Alloys for them. I also think that the mirrored hull is UTTERLY WORTHLESS. No, not worthless, WORSE than worthless. Reactive is barely better, and the most expensive by far, both to repair and insure. So I feel that the mirrored needs to be -20,-40,50. Most of an explosion's energy is thermal. It's weaker against the most common type of hull damage, and very strong against the least used damage type for hulls. Reactive should be either cheaper or should be, say, ~20% better off with resistances. E.g. 40,0,-10. It's better in almost all ways, except for thermal, the least likely damage to hull, better with the most common and much better with the less common but more deadly explosion damage.
But the simplest change to HRPs would be twofold:
Resistance engineering would apply ONLY to the HRP module (damage to its durabilty is reduced)
If you stack small modules with engineered resistances, all tht means is you have a cheap repair bill instead of stacking up to, say, 99% resistance, making your hull effectively 100x stronger. This limits the effect of restance engineering making it possible to allow a wider range of resistances and options to play for, what you pick depends on weight, ship durabilty, repair costs and how long you expect to be in combat for.
HRPs intercept a fraction of the damage to the hull, not add to the hull's durability.
If you could add 3000HP to the Eagle via HRPs, it would make no difference than adding 200HP, since the Eagle doesn't HAVE 200HP on its hull. This limits the effect of stacking without removing the options.