If the FBI has been tracking down SilkRoad for years, I find it completely reasonable that they finally find the location of the server just based on traffic analysis. I'm sure that FBI or NSA runs number of exit and intermediate nodes to collect statistical correlations from traffic and track down hidden services given enough time (there is even public research that shows how it can be done: http://epub.uni-regensburg.de/11919/1/authorsversion-ccsw09....).
All that said, its even more likely that they found his identity other way. He seems to have slipped from time to time. I think most people underestimate the amount of boring and tedious chores they must do year after year if they want to conceal their identity from FBI who is actively searching them online. It seems that the main theme in revealed identities seems to be reusing usernames or using the same email in two different contexts that link person to his anonymous identity.
All that said, its even more likely that they found his identity other way. He seems to have slipped from time to time. I think most people underestimate the amount of boring and tedious chores they must do year after year if they want to conceal their identity from FBI who is actively searching them online. It seems that the main theme in revealed identities seems to be reusing usernames or using the same email in two different contexts that link person to his anonymous identity.