Both of their diseases as depicted by Shin (anime) and Itachi (manga/anime) remind me of Tuberculosis (i.e. "Consumption"). The symptoms fit pretty well actually. I don't know what Kimimaro had. Lol at all the amazing things they can do with medical ninjutsu, but they can't come up with antibiotics. Yes, antibodies to poisons, but not antibiotics no jutsu, to my recall.
Note I could be wrong about both the disease (it's only speculation), and I may misremember about whether there are antibiotics.
Peace