I think there are several concerns here - are you asking about a pure MAC hardware system.? And if not, how is your Intel chipset setup made to support Thunderbolt? on the PC?
The most succinct answer I know there is no issue with the bandwidth. But this might depend on your lash-up and especially if you are in the limited edition Intel approved Thunderbolt. I have an Asus board with support but have not hooked up beyond the first connection as it is all I really need.
You would only benefit well from Thunderbolt Level 1 if you plug in a Thunderbolt raid array (typically a $600 US box), and then of course require a raid array to distribute data out at Raid0 speed. Doubt you need that but?
On the other hand you can benefit well from USB3 external to Sata connected drives ( build your own - not the cheap manufactured USB3 portables). Direct Sata 6G will give you the best single drive performance providing you spec tightly on Hitachi or WD.
Not in love with the idea of external drives. I have 7 onboard sata drives now and would prefer to continue with internal based drives. The easiest way is probably just a pcie sata card. That would give me another 4 or so sata heads. Just wondering if it's worth taking advantage of the thunderbolt support I have.
USB 3 off the Motherboard is just as reliable as Thunderbolt hanging - in fact there is really no distinction from running off the Sata6G internal in that regard. Thunderbolt would be chosen for the reason I specified above.
"[I]Not in love with the idea of external drives.[/I]"
I'm not fond of having disks all over the work surface, either, but I do have some for portability. I was surprised that the Hitachi Touro Pro USB3 drive was faster than the internal disks in this test. As a portable, it doesn't get used as much as the other disks but I carry it with me all the time.
I considered Thunderbolt when I selected my motherboard but passed.