I've been working for petsmart for about 3 years. I've worked at three different stores, 2 in NJ and 1 in florida and this is a common practice. They are supposed to use the big Oranda goldfish to clean the tank. It's not our idea, its just something we are told to do. But, I have yet to see any negative effects in my years there. I buy all my stock from work and rarely have had any sort of problems with any of the fish. Yes, we do get snails in the system because this is very common. The snails come in the deliveries with plants and fish and the breed in the filter system since it is a very very large filtration system. The oranda are always in great shape and are separate from comets and rosey reds. The orandas do an awesome job eating the snails for us. In any of the stores I've worked at, we've never encountered any diseases from that practice. Only time a fish gets sick is when it first comes in from delivery which happens to the best of us. I'm sorry to hear about them using comets because that shouldnt be. I am pretty knowledgeable on fish and i've worked with good older friends of mine who have been in the fish hobby for a long time and we've never found a problem with it yet. Like i said though, it's just something I think all the stores do. Even some lfs's near me do this at times.
Hope I've helped in some way.