Patrick Lenz proves that running an SSD over Thunderbolt as your main boot drive is as fast, if not faster, than having an internal SSD:
When I had everything wired up to one of the two Thunderbolt ports of my iMac, I fired up the Black Magic Disk Speed Test and got quite satisfactory results of 250MB/s write speed and 480MB/s read speed, respectively. My Late 2010 MacBook Air, by comparison, clocks in at roughly 100MB/s write and 140MB/s read speed on its internal SSD.
Lenz’s Thunderbolt drive also gets faster read/write speeds than my mid-2011 specced-out MacBook Air (which gets speeds of 230MB/s and 210MB/s respectively).