My limited understanding is that Thunderbolt is basically a transport layer for PCI Express, and TB2 should have enough overhead to be just as fast, even with multiple cards. I bet there are engineers at Belkin and Griffin already working on an expansion chassis full of drive bays and PCI slots that looks a lot like the old Mac Pro box; maybe even with room to put the black cylinder inside it.
I believe the speed of PCIe is pretty much the same as Thunderbolt 2.0: 20 gigabits per second. As such, connecting an external mass storage drive means no loss of access speed to and from the external storage device.