If it's for a non-commercial project such as a school assignment then if you ask the right people in the right way you should be ok (but probably only outside of business hours). If it's for a feature film or other commercial enterprise then they are going to want location fees for the priviledge of filming there, which if you are considering shooting in a major chain store could probably mean dealing with the head office.
For non-commercial stuff you are better off finding privately owned local equivalents of the big stores where you can talk to the person in charge face to face. Kevin Smith filmed his first movie Clerks in the convenience store where he had worked (which was privately owned) and got permission to shoot there when the store was closed, if this had been a major chain store he would have had no chance as he would never have got through to the person who makes these kind of decisions and even if he had they were unlikely to have agreed unless there was some kind of financial incentive involved.
- Everything is copyrighted, such as uniform shirts, displays, logos.
- You may catch something on camera that can be used later to sue the store.
- The city request you to have a permit so they can get some money out of your work.
