Well you own the building but they own the shop. It is like a strip mall, if you own the building but rent each individual shop you still own the building but you cannot simply walk in all the shops and steal from the cash register because you own the building the shop is in.
Also it is considered trespassing if you are in the shop during non open hours or if you already beat the game and, well not to spoil it, the shop keeper is no longer there, at all times.
Shopkeepers must be in the shop, and open for you to not be trespassing. If from some outside circumstance the shopkeeper is not there, whether it be at night or lets say the boogie man got him, you will be trespassing.