It would seem that not all items that are found in a shop is what the merchant has to offer as well as not all the merchant has for sale can be found in the shop.
I think it would have been better had their been a master locked chest containing the rest of what they have for sale. With the key on the person but with a high difficulty to pickpocket.
Also, stealing a merchant's merchandise too often would result in the shop becoming empty (but should be back up and running by someone else in an in game month to one year) and the merchant is now homeless on the streets or simply gone completely.