The only thing that might disturb the balance of the game if the shops were to restock, as far as I can imagine, would be infinite enchant scrolls from the library. However, I say let that be, as it would require truckload of grinding and patience to buy enough of them to encahnt all your gear beyond reason.
I always thought it's much better to squash all easy to exploit bugs than to try to stop hevay grind player - they will always find a way and many of these changes are just killing some fun for the majority, who will never grind or farm too much simply because it's boring.
If anyone was determined to follow Mellis by becoming the world's greatest trader, I say let them mine whole dungeon levels and sell the rocks and stuff to burn through hundreds of enchant scrolls chasing utter overpoweredness - they earn it if they can keep doing this for as long as it may take. It's already possible to enchant your gear to very high levels with a wand of cloning/mirroring, so adding more scrolls will not change this much, as they tend to work extremely rarely when you reach higher enchantments.
But if enchanting is still concern, items could be made to explode from overenchanting - until +9 you're safe, but then every successful enchanting may break or outright destroy the item. No, it does not prevent eternal grinding, because I hate preventing options. But it makes it much less worthwile.