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.
Thank you for the clarification. I've probably read it too fast.