It's easy to understand why the price went up of *existing* stock, because there is no distinction between the HD in the shop, and the HD further up the supply chain. Hell, the value of *your* HD went up too. It's not that there is some magically expensive hard disk further up the supply chain and is waiting to be conveyer-belted along the chain.
By value, I'm talking about "what the market is willing to pay for it", not "what the retailer bought it for". In many instances, the retailer doesn't even "buy" the stock to sell to you, see Sale or Return for an example, and quite probably iPads in authorised resellers (if the Apple NDA allowed us to find out).
In fact if the supply chain as a whole didn't increase its value, it would get even more complicated, as different shops would have vastly different prices depending on when/where in the chain they are.