I'm one of the authors. You are right, these are the only onion services that were most likely targeted. The others are part of our publicly available dataset, but most likely false positives.
There is a file called targeted-onion-services.tar.xz which is provided at the end of this page. The excel document inside, once removing duplicates, matches fluxist's comment.
This is good work. Just like a competent IT department should pen test their own network, Tor needs white-hat hackers working to shake out the vulnerabilities.
Great work and paper. The fact 53% of the Tor relays have either shared prime factors or non-standard RSA components is worrying. This kind of research is mandatory.
You are misunderstanding the summary. Researchers found ~3500 keys with shared factors in a historical dataset of ~4M keys. None of the relays with vulnerable keys they found are online today.
https://lists.torproject.org/pipermail/tor-dev/2017-April/01...