Hidden services are still secure, presumably, because there is no exposed section of the network to inspect. All they can do is monitor and do statistical analysis, and maybe mess with the traffic to try to get more ideas of flow.
httpd > tor node > tor node > tor node > rendezvous point < tor node < tor node < tor node < client
There's practical attacks for enumerating hidden service public keys, and so I wager that there's somebody somewhere with a complete map of the real server locations as well.
[1] https://metrics.torproject.org/users.html [2] https://metrics.torproject.org/network.html?graph=relaycount...
The bigger protection is the ease with which the NSA can mount this attack on TOR. I have no doubt that they could do it, however I do question if they can do it on a massive scale.
Think you're getting your entry and exit nodes mixed up there. Tor chooses a small number of entry nodes (entry guards) and attempts to only use those.
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.
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.
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.