You could make the effects of intoxication more powerful, or make dwarves more prone to brawling.
Is there a tag that lets creatures move through stone, like ghosts do? You could mod creatures like giant worms or giant moles or tunnel dragons to be able to dig through the rock and appear in your fortress even if it's walled in.
Vermin syndromes seem promising, but kind of boring if they just make you sick. Vermin that can start fires or cause dwarves to mutate or raise undead would be more interesting. It would be interesting if you could mod some kind of a two-stage lifeform that could burrow into the fortress as a vermin, then lay eggs in your foodstockpile or wherever that hatch into larger dwarf-eating predators, then lay vermin eggs. I think some fungi and slime molds have similar lifecycles.
You could make the underground crops toxic in high doses, so if your dwarves are only eating plump helmets, they'll get a plump helmet high or something. Underground crops could slightly cause it, overground crops could slightly cure it and meats could be neutral. Off course, you could still wall in your overground crops, but it makes certain strategies a lot more difficult.