First: illness and complications based on the type of work a character is exposed to. Such as miners getting respiratory infections which could progress to 'miners cough' and require medicine and/or bed rest to fight off. That would lead the player to have to make divisions on the health and well ring of their people. Or possibly if you have captured slaves working the mines, the lack oh care. I'm sure there are stronger examples of cause and effect illnesses but that's the main one I could see that has a place right now.
There is also the effect of dead bodies and waste from machines/ production would have over long periods of exposure to your citizens. This would for e he player to research effective methods of waste and body disposal, or just create dump pits and pray that it's far enough away from your population.
Second: Event type diseases or 'plagues' that the player would have to utilize his scientists and researchers to find and develops a cure. This could be a long drawn out event and could create some very interesting cause and effect gameplay. Like for example lets say that the player is the first to develop the cure, who so you sell to? What if people can't afford it? The production wouldn't be free. This would lead to desperate factions attempting to desperately raid you or the wealthier towns in attempt to cure themselves. Or perhaps vice versa, say an enemy faction developed it and hordes it to themselves and their allies, would you attempt to desperately negotiate or use military means?
I apologize for my rant and probable spelling mistakes. It is very late here and I'm typing on my phone