depends on which direction you will install your cooler. If you do it lets say horizontally like in the picture then yes you will have the same problem. But if you do it vertically as I have set it up you only lose the slot nearest to you cooler.
You don't have to mount the cooler as shown in the picture. The picture shows it mounted in a way that the fan will push air towards the PCIe port.
If you mount it in a way that pushes air towards the back (like most people do), you won't have much problems with it. You may have to raise the fan up a little if you have clearance issues.
And unless you live in Asia, or import one, you won't find the Hyper 212X for sale.