For one, while right now it leads to nowhere, there is a Hearthstone link, within the Hearthstone section of the store, which looks like this. Like I mention above, this, unfortunately, just leads you, via a series of clicks, through an information page back to the beta sign-up.
Nonetheless, we heard at BlizzCon that Hearthstone will hopefully be in open beta within a month, and it seems likely that when that time comes this will be how you procure it.
Another interesting note is that all the WoW in-game services are now on the battle.net store for purchase. Name change, faction change, all those things, including things like the Scroll of Resurrection that are currently free services. It seems likely that the battle.net store will become the central place to manage paid services from, and this is a great change. It was confusing to have to go through your account and add services to do some things, while you had to go to the store for others.
And it seems highly likely that before long the physical items will return to the revamped store. In the meantime, I hope you got what you needed from the previous version!