Thunderbolt/Lightpeak has a lot of potential because of the high bandwidth and lower latencies. Those attributes would certainly be a major advantage over USB for accessing external HDDs, however, I don't think it is as much of an advantage over eSATA.
Currently USB is such as de facto standard in the external storage arena and is so widely adopted that it will take a while for Thunderbolt to reach a high level of market penetration. I really have to wonder if Thunderbolt will go the way of Firewire, although given Intel's weight and ability to integrate it into their own chipset it does seem to have a better shot.
To answer your question I wouldn't be ditching USB 3.0 and eSATA anytime soon, although it may not be a bad idea if upgrading in the future to upgrade to a platform that supports Thunderbolt.