Ah fair enough - I know the Asus X99 Deluxe motherboard I have has a Thunderbolt Header which needs an addon card/module to actual supply the ports.
External drive wise - we've had good experiences with Drobos (I've currently got a Drobo 5D USB connected to my Linux machine and will be moving it to my Raspberry Pi once I fully migrate to my PCS Windows machine: Drobo's only support a single format standard - so ext3, NTFS or Mac OS). My wife has a Drobo Mini connected to her Apple Thunderbolt display which is then connected to her Apple Macbook Pro which is running Windows...
Drobo's aren't the cheapest external drive solution, but does allow for drive failure (rebuilding a 12Tb+ ext3 array does take a few days after drive replacement) and additional larger drives "automatically" increases the RAID size.
There are some external Thunderbolt enclosures you could use with "any" drive (usually SATA in 2.5" or 3.5" sizes: differs per enclosure), but I can't really recommend any at the moment as I haven't tried them.
I think the slower sata 2 ports are faster than a mechanical drive.