In FR, there are magic shops that only sell small items in Red Wizards Enclaves. Since they are pretty much fortified embassy complexes that need to be massively protected anyway and are under harsh Thayan law, theft is less of a problem.
Thus, it is good to associate magic dealing with powerful organizations who can offord the risk of theft, but at the same time have well-protected areas and a long reach for revenge, shop of no shop.
And note that few permanent and powerful items will be stocked at such stores. Instead, they likely have contracts with craftsmen (for masterwork items) and spellcasters to have items manufactured on order.
A PC in my game runs a company that markets and either makes or comissions through contracts, all items manufactured by the crurch of Mystra in the North. The church itself highly wards the store, and backroom deals with the local Waterdeep authorities give it especially good police protection. However, nothing particularly powerful is housed there, as primarily, the shop is a showroom for mgical items that stocks only inexpensive items onsite, with all magic kept in a vault at night.
Everything else is delivered to the owner or picked up somewhere safe. The owner has arranges that the most expensive items be stored (until delivery) and picked up at Blackstaff Tower, another use of the idea of utilizing already heavily-fortified locations
