Make the capital repair modules require mineral blocks as fuel, in similar fashion to fuel blocks. So there is a cost to running the big ships instead of just the fuel needed for jumps. In real life ships do need regular maintenance, so there should be a regular fuel like tick on the mineral blocks. While the ship would continue to work without them, the ship would degrade, its HP slowly reduce.
While the shield based ships could rely on their shields to take the damage, eventually even they would have hull and armor made of tinfoil. So even though you can produce a massive fleet of capitals, it would demand keeping up the effort to keep them running. You could mothball capitals, but to get them back into flying order, you would have to essentially rebuild them.
I think 10% of ehp a month would be a sufficient pace for this, that would begin as soon as the fuel bay is out of mineral blocks. This would mean in 9 months the capital ship would be as good as a glass cannon, but the ship would never degrade to all the way to dust. Lore explanation could be that the emergency structural integrity fields would keep it intact enough, but after that 9 months you would need to provide 90% of the minerals in their block form required to build the ship, to get it back to 100.
Also these mineral blocks would drop when the ship is killed, so in a fleet you could risk bringing glass cannons into the field, in the hopes of scoring enough mineral blocks to get your ship to full power.
What this would do, is that it would force major alliances to decide the usage of their resources more effectively, no longer could they just build massive fleets of titans to sit idle in some keepstar, in case they are needed. As they would need to constantly feed them minerals to keep them operational, alliances would have to make strategic decisions on what fleets they have capacity to keep operational. You could have your 100 titans, if you have the capacity to feed them the minerals they need to be functional, or let them become glass cannons that would die essentially as soon as they get bumped.
One block would not just be X units of trit but a mix of all the minerals and couple more exotic things in EVE, just like the fuel blocks are mix of PI and ice materials. I don’t really see a need for multiple kinds of mineral blocks, one kind of a block would be sufficient.