I was happy with the addition of Size 1 Compartments because I can cram another utility module in, but the complaints of Health inflation were certainly valid. It makes me wonder, why not just implement the reverse of Military Compartments with Civilian Compartments? The added Size 1s would be prime candidiates. Would allow the possibility for ships to have more utility without inflating Health.
The boat has sailed. The limitation would've made perfect sense when those slots were introduced. The suggestion was made at that time, it was ignored.
By now the slots are filled. So what should happen with the new restriction? Should the slots be automatically emptied? Then people loose equipment. Affected people will be unhappy. We don't need that.
Should equipment there stay? Then i'll just leave my armour in those slots, never to remove it again. A permanent advantage for me. But unfair towards new player, so again a bad move.
So unfortunately adding the limitation now, so much later, is not reasonable. But as others already expressed: the problem are not the slots themselves. A mere un-engineered C1 HRP makes very little difference. It's the fully engineered C1 HRPs which matter so much. So really: hit engineers with the nerfbat and hit them hard. That would solve a number of issues the game has and improve the situation a lot. I just also know that FD doesn't dare to try that again.