I wouldn't worry about the stores running out of stock to fulfill reservations. For all the hype about 20K+ per hour, 91K first day sales, there will, at the very least, be plenty of iPads to fulfill all the pre-orders and reservations. Stores will be shipped iPads for stock based on reservations made for pickup specifically at that store.
I'd say that if it they get too close to the number they will have on hand, Apple will just stop allowing pre-orders and reservations on line at that time.
That said, my gut tells me that it's a go thing I reserved one. I don't want to go home empty handed and I begin to wonder if they'll be in short supply after all...
My head, though, tells me that this is silly. There will be plenty to go round. This is:
a) a good way to hook customers into committing to buying while the hype is hot.
b) a good way to avoid mobs of people trying to elbow their way to the front of the store to get one on launch day
c) <this one contradicts b> a good way to make sure they will have calm, orderly lines of happy people camped out in front of the stores (but only for an hour or so) so that the news crews can get some good footage and increase the hype.