Yes, it does. Also, Thunderbolt (1 and 2) supports SATA NCQ, which USB 3 historically has not. This is fixed with USB 3 UASP enclosures, but... (editing this after some reading since I was unsure if the iMac supports USB3 UASP and it looks like every Mac with USB 3 supports UASP)
You can read about USB 3 UASP here
http://www.tomshardware.co.uk/usb-3-uas-turbo,review-32467-4.html
Anyway, the difference between the same drive in a normal USB 3 enclosure and in a Thunderbolt enclosure is there, even with a 7200 RPM mechanical hard drive, especially when copying multiple files. But I am pretty sure that the tom's hardware review that proved this did not use a UASP USB 3 enclosure, as I don't think they were available yet. I'll look for the article again to double check.
Having said all of that, in the quest for fastest and best, people forget the most important thing:
In real life and in typical use, a normal user would not see the difference between an SSD in a Thunderbolt enclosure, an SSD in a USB 3 enclosure or an SSD in a USB 3 enclosure with UASP. A typical user would also not see the difference between a "fast and expensive SSD" and a "slow and cheap SSD", unless your typical use includes running artificial benchmark tests to check your drive speeds all day
Final comment: if you wish to check if UASP is working, then connect the USB 3 enclosure, open the terminal and type in
Code:
ioreg | grep IOUSBAttachedSCSI
If you get nothing back, then UASP is not supported by the Mac, or the enclosure, or both. If it is supported then, you'll see something similar to this
Code:
| | | | +-o IOUSBAttachedSCSI <class IOUSBAttachedSCSI, id 0x100003187, registered, matched, active, busy 0 (2504 ms), retain 9>