Have you seen the Tor document on how a Tor Hidden Service works?
Essentially, in the same way that it's hard to find the source of traffic from a Tor exit node, it's hard to find the server operating a Tor Hidden Service. Authorities can't shut down the server, because they can't find out where it is.
The .onion TLD is not really a TLD (so there is no domain registrar to shut down), but it's recognized by Tor.
There are other methods for tracking it down - checking cash flows, poorly anonymised Bitcoin transactions, even good "old-fashioned" anonymous tips to the police. So far it seems none have been sufficient.
Ah, I think I understand the confusion. You're expecting that by flooding the Tor network with malicious exit nodes, you'll eventually create one that's used for the "exit" to a .onion. You'll know it's the target (e.g. Silkroad) because you'll be able to see the traffic contents. This does not work against .onion hosts, because unlike an exit node connection to a "normal" host on the public internet, traffic to .onion hosts is end-to-end encrypted.
So even a malicious exit node does not know that it's connected to the Silkroad host, because it can't see the traffic content.