With players approaching the level where magic items are more affordable, here's what I've implemented in my campaign:
- Consumables, primarily potions, are manufactured by the two gnome brothers. They don't label anything and they're confirmed pyromaniacs. Stealing from them would be quasi-suicidal. Only a few locks prevent mundane thieves. Common sense stops everyone else.
- One or two NPCs have some magic items they sell. These tend to be high-level characters who have little to fear from common thugs and lower-level adventurers. Anyone stealing from them will either be killed quickly or -- should they succeed -- no longer have a ready source of magic items. Examples include the 2nd highest level cleric in the campaign area and the other is the highest level warrior-type in the immediate area (excluding monstrous NPCs, of course).
- Practically everything else is commissioned. Cash up front, in advance for full service. The commissioned item will be ready in the appropriate number of days, not before, almost nothing is kept on-hand. This allow me to restrict availablity vis-a-vis things I don't want in the campaign, and increase interaction with the NPCs. Some of them like some of the PCs more than others, some like them less, this all is reflected in the availability of the crafter... "I'm sorry, I'm booked up until next Christmas, let me put you on the waiting list." I can also extort more cash from the PCs... "A rush job? That'll cost you."
In other campaigns I've seen a few magic shops schemes that work well. Most of them rely on high-level spellcasters to thwart theft.
Hope that helps,
Greg