Yes, the values of health decrease by most of the illnesses are totally wrong and do not fulfil their purpose at all.Just checked the values in the code out of curiosity, and apparently the great pox penalty is just -1 health (which is pretty amusing since it means a perfectly healthy ruler who's normally ~5 health would only be ~4 health which is hardly a problem in CK3). Anyways, would explain why the negate health bonuses of the food is pretty decent, as the bonuses can range from 0.1 to 0.4 depending on the quality of the artifact (so if the ruler by chance has the rarest quality for both, it'll be 0.8 of the health penalty that's offset). I'll make a note to nerf that for the next update, thanks!
I coded very simple and direct specific events in my mod to address each illness that once fired, kills the character in question. Of course, the chance of each event happening every year is much different from smallpox to cancer or leper, for instance...