At night when the NPC is sleeping, walk into his/her shop and locate the shop-chest, but remember to not steal everything or the storekeeper is put out of business.
That's actually a really cool idea. Permanent consequences for thievery! I imagine if Skyrim had something similar, like seeing a shopkeeper NPC get turned into a beggar after going out of business (by you stealing from him too much), I may have reconsidered pilfering everything in sight.
