Gently nerf the ability of pets to steal from shops, so that a player with a stack of meatballs or a magic whistle can’t clear out an entire shop. Suggested ideas:

• Make apport less easily exploitable, requiring more in-depth training than just feeding your pet after it drops items next to you.
• Track the total amount of value lost to a shop by a pet moving items out of it. Once this value exceeds some threshold, the shopkeeper intervenes, either by turning hostile if you continue letting your pet steal after a warning, or attacking the pet.
• Track items that have been stolen from a shop (probably by marking them with the monster ID of the shopkeeper). You can’t resell stolen items; the shopkeeper won’t offer any money for them, instead they will grin and say “Thank you for returning my stolen [item]”, taking ownership of the item. However, this doesn’t solve the problem where you really do want most of the shop’s inventory for yourself.

If possible, work in a “pet-ty theft” YAFM somehow.