Juan,
I agree the old adage that we are taking care of our water parameters more so than its inhabitants to be true. If we keep consistant parameters, QT, don't overstock, have plenty of hiding spaces, feed well, etc. our animals will thrive. Unfortunately, we have a artificial enviroment that can never duplicate the ocean. Thus, disease and what not have to be addressed. In your case, you nipped it in the bud, but from my understanding cryptocaryon has to run its course without any host. This means running the tank fallow for a few months. Now, as a fellow "large tank" owner I know that's next to impossible. It seems the current fish have built a tolerance to the ich, but introducing new fish of course won't. If you could catch one fish and do a skin scrape (literally taking a skin sample with a blade) and placing under a microscope, it will be the only way to tell if the fish are still infected.
Maybe contacting a fish vet would help ?