Magic shops as encounters

Shoplifters will be electrocuted.

If you absolutely must have magic shops in your campaign, then consider treating them as encounters, with appropriately powerful guards and wards for magic merchandise. The examples here, calculated using Pathfinder core rules, show the rapidly escalating levels of deterrents required to match a challenge rating to the items on offer. This may dissuade you from making many items readily available for purchase, but if not, might at least prove useful when dealing with chaotic evil player character parties.

The hunting village

Base item value 500g. Minor items: 2D4 (5). Medium items: 1D4 (3)
Minor items: L1 potion of longstrider, L1 divine scroll of magic fang, elixir of hiding, +1 leather armor, efficient quiver.
Medium items: +1 longbow, +2 studded leather, +2 amulet of natural armor.

Total value: 17,000g+
Equivalent encounter CR: 13 (fast advancement).

Protected by: L8 wizard, L6 ranger, CR 2 spiked pit trap, CR3 acid arrow trap, 3 guardian scrolls (CR3 each), 4 dire weasels (CR3 each), 4 living topiary (CR 4 each) and a pact with a moon dog (CR9).

The small mining town

Base item value 1000g. Minor items: 3D4 (7). Medium items: 1D6 (4).
Minor items: L1 arcane scroll of floating disk, L2 bull’s strength potion, mithral shirt, +1 heavy pick, ring of climbing, belt of constitution +2.
Medium items: +2 breastplate, +2 warhammer, goggles of night, belt of dwarvenkind.

Total value: 47,000g+
Equivalent encounter CR: 17 (fast advancement).

Protected by: L10 wizard, L7 fighter, 50′ spiked pit trap (CR 8), cone of cold trap (CR 11), 2 stone golems (CR 11 each), and 2 iron golems (CR 13 each).

The small port city

Base item value 4,000g. Minor items: 4D4 (10). Medium items: 3D4 (7). Major items: 1D6 (4).
Minor items: L1 potion of comprehend languages, L1 arcane scroll of animate rope, L2 potion of levitation, L2 arcane scroll of gust of wind, +1 studded leather, +1 buckler, +1 scimitar, ring of swimming, feather token (fan), feather token (anchor).
Medium items: +3 leather armor, rod of flame extinguishing, trident of warning, staff of charming, ring of water walking, pearl of the sirines, L3 pearl of power.
Major items: Plate armor of the deep, +3 anarchic rapier, orb of storms, apparatus of the crab.

Total value: 300,000g+
Equivalent encounter CR: Three CR20 encounters (fast advancement).

Protected by: L15 wizard, L10 bard, hail of arrows trap (CR9), lightning bolt gallery trap (CR17), 4 coral golems (CR9 each), 3 adamantine golems (CR19 each), 2 cannon golems (CR15 each) and a bound elder air elemental (CR11).

These examples assume a single store per settlement, but larger locations would be more likely to have items on offer split between businesses. The shops may be run by aging, retired adventurers, most likely with a squad of minor assistants and a number of low level wards or curses to assist in protecting the stock, and divinations to help locate stolen goods. But the challenge rating of a store does not necessarily just have to include its immediate protections.

Owners may be allied with other powerful characters to help hunt down thieves, or in larger settlements, they may rely on local guards with a few elite officers and investigators. Traps and guardians of significant power, such as golems, may be leased from an arcane guild with agents across the kingdom. Such an organization may take a swift interest in anyone who thwarts or destroys their security measures, making life much harder for a merry little band of murderhobos.