The "hacking" was speculation on the defense's part when they filed their motion in August. If you read the motion[1], because the defense didn't yet know how the FBI located the server, Ulbricht's lawyer wrote a long statement speculating that the NSA/DEA was providing the information to the FBI through parallel construction. The defense did not show any proof of their accusation.

A month later, the FBI gave sworn testimony[2] indicating that they found the server because Ulbricht had failed to configure it properly and it was leaking out its actual IP outside of Tor channels. There hasn't been any proof shown that the FBI hacked his server. A number of people have claimed in the past that they came across the actual IP for Silk Road's server as a result of misconfiguration[3][4], so frankly it doesn't surprise me at all that the FBI also found a leak.

[1] https://www.scribd.com/doc/235692879/Silk-Road-4th-Amendment... (starting on page 40 of the PDF - the page number in the document itself is 28, entitled "The Searches and Seizures In This Case Failed to Satisfy the Fourth Amendment")

[2] same link as my grandparent comment (https://www.scribd.com/doc/238844570/FBI-Explanation-of-Silk...)

[3] http://www.reddit.com/r/SilkRoad/comments/1b1lvy/warning_the...

[4] http://www.reddit.com/r/SilkRoad/comments/1dmznd/should_we_b...