Dark sites of all types still continue to run uninhibited for the most part. From my readings, the major or at least known/researched security holes have been plugged already by the developers, and the rest of convictions have happened because of user error, not the technology involved.
If memory serves me correctly, one particular pedophile abuser was caught after years of being investigated because he was identified through skin marks (I want to say it was freckles on his hand, though I don't recall the exact details of the article) that led investigators to him, not anything technological.
I'm a proponent of total anonymity online because it allows for whistleblowers to leak information that is untraceable to them (again, without consideration of human error). In the case of Wikileaks, for example, even though they weren't on an anonymous network, it still led to the largest classified information leaks known, from NSA tools to national and international communications between heads of states, diplomats and everyone in between. The general consensus was that it was a good thing. I don't necessarily agree with that, but one can't discount its value.