The one thing I could see Bethesda not putting in respawning shops would be the fact that it would make the game extremely easy, financially. What they should do to keep the game interesting and fun for thieves is, first, yes. Start out with merchants placing good stuff on their counters at night. But after the first break-in and the merchant discovering a stolen good, all of the locks (including the one to get into the shop) should go up a rank. As well as all of the gear on the counters being replaced with something that is less valuable. So say, day 1: You break in and steal an Elven helmet. The shopkeep comes in that morning and realizes an item is missing from the room. Upon that realization he could go to each "spawn point" and take all of the items off the shelves. Then go back through the "spawn points" and replace them with something else, so it would go from looting something, say Elven, to something like Steel. And this would continue until you reach the lowest tier, where then it kind of caps at an all time low and you can continue to loot fur or iron junk all the time. But the limiting factor on looting low-tier equipment all the time is the locks are gradually more difficult until all of the locks are 'very hard'.
Also, if there are some unlocked containers in a room, after a few nights of burglary the containers with no locks could be fitted with locks. And to even further increase difficulty, the shopkeep could hire a guard to patrol the shop, adding another fun factor to stealing. Of course the ultimate outcome of robbing this store as many times as it would take would be: Very Hard locks on everything, Lowest value loot on tables/counters etc., and a guard patrolling the store.
Sorry about the jumbled mess of words, that is the first paragraph
Note the use of "elven, iron, steel" etc. is to signify the tier of the loot being placed.