Perhaps I was unclear. When I say an agency can issue a subpoena, I mean exactly that: rather than requesting one from a court, an agency can issue one under its own administrative authority - within the limited scope authorized by statute. The IRS can subpoena your bank statements, say, or the EPA could subpoena a suspected polluter's freight delivery data. Many agencies have limited powers to investigate and then prosecute or impose financial penalties, otherwise the court system would need to be considerably expanded. After going through any dispute/appeal process of the agency, then a matter can be heard in state or federal court as appropriate. It's good to get proper legal advice and do everything in writing from the beginning, or you can waste several years fighting the inevitable!

The 'preferred method' mentioned in the Hotwatch briefing does involve going to a judge too, but that's for the separate purpose of getting a secrecy order to avoid tipping off the suspect. The government did get a lot of new powers to investigate things under the PATRIOT act. Though some expired or were amended later, civil liberties were a low priority in October 2001 when people were still feeling panicked about terrorism.

I agree that the DoJ should call back and say 'we're looking into that, give us a few days' - but you know, people would find a reason to be paranoid about that too. Newspapers used to say 'had not called back by press time,' but with blogs that might mean anything, such as waiting only an hour (I consider Wired a responsible news source in this respect, but I still don't know how long they actually waited, and would sort of like to). Remember this Hotwatch powerpoint is 5 years old, and agencies are being told to tighten their budgets a great deal lately; press & public relations departments are often the first to see cuts because they're considered 'fluff' expenses compared to the core mission of a department.