Absolutely not. The government is not one unitary piece. The NSA is not the ATF is not the FBI. These capabilities were likely kept secret from other governmental agencies as much as the public.

Furthermore intelligence agencies are well aware that every action communicates information back to their adversaries. It's a no-brainer to let Silk Road exist if you think doing so gives you the edge on terrorism, or otherwise furthers the national interest.

Silk Road is a few pennies and few gram transactions. [See the data here http://arxiv.org/abs/1207.7139] It would be foolish to expose their snooping capabilities for this, right? Wow, Tor is not considered safe... Amazing

No way. What you forget is that once they bust it -- then they've REVEALED that they have the capability to do that.

Once they've revealed that, then people take account of it, and it becomes harder for the NSA to monitor them.

Half of the signals intelligence game is keeping your capabilities secret, so you can keep monitoring the signals, rather than have your target change their game.

That is to say, if they can get into Silk Road, then they probably ARE already monitoring everything that happens on Silk Road, and they'd rather it stay UP so they can keep monitoring the people on it (being very careful never to reveal that they can monitor it), then bust it so the people go elsewhere.

If every police officer had access to these tools, the news would leak much sooner.

So I would think these tools are available only to a select few, and those are more interested in more high-profile tasks like catching extremists or going after political opponents.

I, frankly, don't think SR is that high on government list. Not yet.