I think that TOR should no longer be considered secure in the wake of so many busts. Either it isn't secure by some flaw, or it is too easy to fingerprint visitors, or some other work around.
There are some interesting theories being tossed around. I'd like to add one more. The common thread across all darknet websites is the fact that they generally run from datacenters. Most people don't host websites from their residence. Further, most people don't colocate servers anymore. I would be surprised if any of the 414 websites operated on boxes that had been colocated. However I won't rule out that colocatin…
If you're doing this under a warrant, you could just request that the server's operator unlock the machine. Whether you comply is a legal situation that varies from jurisdiction to jurisdiction (in the US, it seems that you might be held indefinitely in jail if you refuse to divulge your key). The thing is, you should be able to make an extremely strong case (possibly with the EFF's help) that any warrant is false. Anonymous traffic itself should not be enough to compel you to divulge your secrets without other evidence pointing to your machines (standard IANAL, but this seems consistent from everything I've read).