In my area, Petsmarts run all their tanks on one system, except the invert tanks. They treat the system with a preventative dose of a copper med. The Petcos here don't use preventative meds. I've bought fish from both, with no real problems. Before buying from any store, it's important to closely inspect the fish, watch the fish eat, and don't be afraid to single out the fish you want.
My small town super Wal mart actually has an employee that knows what he is doing regarding fish keeping. Wal mart tanks are also on one system. He allowed me to inspect the filtration system located directly underneath the display rack. I was surprised to see two enormous bio wheels rotating over a stock tank sized basin. He advised that they medicate fish on a as needed basis; no preventative dosing.