That depends on the owner and the specialty of the store. Most pet stores are just that - pet stores. They may have a fish section, but they are primarily dry food and pet supply stores. They really aren't that concerned about their fish stock and leave that part of it to their fish department manager to handle. These types with a good manager and subordinates that have been in the hobby for a good while know how to balance their stock even with varying bio loads. It's simply water testing and moving around mature media when needed to balance the levels. Then there are those fish emporiums whose specialty is aquaria. Most of these have centralized systems (usually a fluidized bed filter) with UV sterilizers to kill any potential pathogens that can handle varying bio loads. Even these though if not monitored correctly by properly trained and experienced personnel can go bad fast.
In the end, you need experienced, properly trained staff who TEST DAILY, FEED PROPERLY, and CHANGE WATER REGULARLY just like in home aquaria. No one likes to buy stuff from a shop who has dying disease ridden fish. Shops often receive fish already diseased from their suppliers, and it's important to never sell these fish to your customers. Simply label these fish not for sale and treat them for the full course before selling. Always do a dead check BEFORE opening, and every hour while open. When a customer sees a dead fish, it's a red flag against your fish department. Best not to get too many of those.