Are you a Battletech table top player by chance?
No, have enjoyed naval history/fiction and wargames for most of my life. I play UA: Dreadnaughts currently, watch Drachinifel and Dr Alex Clarke along with other documentaries.
Some of the latest thinking about the loss of the Hood I have watched is fascinating. It seems the Hood was really unlucky in that it was turning at speed causing a wave, exposing the lower part of the ship at the time when a shell hit it there. In other circumstances, the water itself would have mitigated the hit/penetration.
This example shows that a hit in the right place, even if minor, could be deadly. Transferring over to Elite, the rules should factor in anyone filling their ship with hazardous stuff should expect to suffer. Of course they could add armour to the magazine hold etc.
Then you would have to think about the replenishment mechanism. That too would be vulnerable.
And why not make hits on missile racks etc cause the detonation of ordnance.
This is a rabbit hole that should not be gone down. Keep things simple. Synthesis works fine. Materials inert until required.