all secret TOR services were warned they were discovered months ago but some didn't protect themselves
only 27 servers with 400 secret services were downed by an international police action
why not so many more - even if some are the biggest for the moment
and where did they get their information because TOR is supposed to be uncrackable (nothing is over time - it all depends on the effort one wants to put into it)
well here is one possibility - and even if they didn't get the information directly from the researchers - it is possible that they have learned how it was done and combined it with a lot of other new attacks against bitcoin and tor that were known for years but only got some perfection and ameliorations the last months
Researchers for example were earlier this year succesful in cracking the anonimity of hundreds of hidden services on TOR and were about to present their results on conferences but had to withdraw after an enormous uproar started in the online community. Those two paragraphs are the most important of that episode. Before they said that de department of defense didn't get the result but that it was possible that the FBI or DHS got it (but they didn't say by which (in)formal way).
"He warned then that "users who operated or accessed hidden services from early February through July 4 should assume they were affected."
Dingledine said the physical locations where the hidden services were housed could have been exposed, although probably not which content was viewed by a visitor.
so any hidden service that didn't move since months and is does criminal action will have to move