I'd like to read up on the research he is basing his opinion on, do you happen to have a link? To me, it sems pretty simple. Ich cannot live without a fish to host it and its cyst's life cycle is fixed. Unless the cyst can put itself into hybernation or something equivalent, I don't see how this can happen. I have never heard anywhere that a cyst can hibernate.
I just did some research on what Fenner says....
About "Crypt Free" Systems:
"There are such things, but unless the aquarist is diligent in altogether excluding these parasites through quarantine, treatment outside their main displays, most aquariums will instead host latent infestations... with discernible populations of Cryptocaryon coming to be through environmental challenge/s to their fishes. In actual fact cysts of Cryptocaryon can stay viable for a few to several months, hence ultraviolet sterilization, use of biological cleaners, allowing systems to go fallow... only decreases the number and virulence of these parasites. Once in a system, the system itself is infested and the only practical means of control becomes providing an optimized and stable environment."
He's saying that the cysts will eventually die in a fallow tank. What the article I read doesn't say is how long they can potentially live. "...a few to several months..." is vague. It would be interesting to know who did this research and how long these cysts can live for.