I am no expert, and hopefully someone will correct me if I am wrong, but given that ball pythons are so prone to showing signs of stress (balling, not eating, wandering...etc) I would think that if he is in pain you could tell. If he is curious (tongue clicking, calm exploration) and seems comfortable (a good eater, a regular sleep/activity level and schedule) I would think those would all be good signs that he is not in pain. From what I understand, IBD is an extremely painful disease and is always fatal. A snake with this condition would surely not behave like a normal happy snake. As for any other condition, I suppose you would have to guage it the same way you would with any animal, watch their behavior and if they seem distressed and nothing has worked to improve their condition consider intervening. Have you handled him much? What was his temperament like?