Well, whether or not it was related to being at the vet is unknown. You could have a thousand snakes go to the vet and get stressed in the same way and yet recover. I think in most cases (this was a thread here) that most of our snakes are harboring crypto and it remains a dormant asymptomatic disease. Much like a lot of the bacterias we carry in our bodies. Some animals for whatever reason, stress, a depressed immune system, whatever, will end up with the active form of the disease. As stated though, I understand that even if they have it, you can sometimes test negative for it and it requires 3-4 tests to confirm. The oocytes have to be present to test positive and they don't always shed them at the time you're testing.
One question though: How big a snake was your 3 year old? Was he undersized or about average for his age? There is a variable in size, but most 3 year olds run about the same size give or take maybe 6 inches. I'm just wondering if he was a case that just maybe never thrived even with perfect care. I know he was eating and such, but was he growing normally with the food he was getting etc? Just trying to see if perhaps there was something that might point to his not surviving.