There is a great problem similar to seeds-turned-rot problem on the surface in caves which I'd like to call "minerals plague". Earthquakes that happen down there are both good and quick way to obtain minerals. However, if you stay in caves for a while, it quickly becomes overwhelmed with minerals lying around. However, that is not all - moleworms drop too and they collect minerals in their burrows before next earthquake happens. There's seemingly no limit to how many moles an area can contain and as time goes by, more moles drop, more burrows are made and more minerals are stored in them. Points of interest like cave bases become overrun with mole burrows which store up to 50 stacks of minerals PER BURROW which in return causes incredible lag.
With that being said, I suggest removing periodic earthquakes and replace them with renewable stalagmites. Stalagmites would regrow from stage 1 to stage 3 during rains and stay at the maximum stage until mined, preventing mineral overflow - you only mine them if you need minerals. If you don't need them, you let them be. Stalagmites only appear in places where they originally existed and don't appear next to structures (similar to world regrowth). This would additionally solve a problem of fossils not being renewable, as stalagmites have a chance to drop them.
Earthquakes as mechanic should stay and still happen due to explosives or toadstool stump attack. Since it would take some effort and resources to trigger an earthquake, I believe it would be fair to have a tiny chance to get rare gems (green, yellow, orange) and thulecite fragments.
Additionally, if world temperature is below 0 (usually during winter) and the stalagmite is about to form, it would have a chance to become ice stalagmite which would be a counterpart to ice boulder on the surface, resulting in renewable ice in caves.