Re-read the complaint. It doesn't say that "FriendlyChemist" claimed to have hacked into the SR system. It says that he claimed to have hacked the computer of a large SR vendor.
While it's tempting to believe that FriendlyChemist and redandwhite were under cover agents, there is no reason to not disclose that in the complaint if that's the case - indeed doing so would actually bolster the strength of the complaint.
If you've read the Silk Road forums, you'll know that it's like any other community, users come to regard people as "friends" relatively quickly and they seek to establish closer ties with the more powerful figures within that community - whether DPR, the admins, or the major vendors. DPR himself courted adoration and approval and he engaged in PM conversations with various SR users using the SR system. It's highly probable that some SR users made their real life identities known to DPR.