I was curious about this, whether or not what a shop had for sale corresponded to what was on display in the shop. So, I went into Arcadia's Cauldron in Whiterun and performed a couple of tests.

I checked to see that she had 3 Potions of Healing on display and 3 Potions of Healing for sale.

First, I bought a Potion of Healing and low and behold, one of the potions that was on display disappeared from the shop.

Second, I reloaded the savegame and stole one of the potions and she then had only 2 Potions of Healing for sale in her inventory.

I thought this was pretty darn cool. It is another example of why I love this game.