I wondered that my self, unfortunatly I bought mine a week ago. But im sure you will get the upgrade free. I was also told by an apple employe at the apple store that the upgrade would only be 10$ so that isnt so bad. 😀
I would think that ipods that are in store when the update rolls around probably will not thave the software on them. I'm sure that the new shippments of them will. So the best thing to do might be to call them and ask what will happen with the update and whether or not the in store ones will have the new update. If they dont ask them when they will get the update and wait for it.