They were legally compelled to add IP logging for that specific user. After this incidence, they went on to obtain a court ruling in Switzerland, where they operate, so that this specific attack cannot happen again. In their blog post about it [1], they instruct concerned users to access their account over Tor.
Of course when Proton say they don't log, we just have to take their word for it. People who don't want that element of trust can use Tor. Personally I believe their story in this case.
It works sometimes. Usually, it requires phone number or email verification. This is important for protonmail to maintain a revenue stream as they don't allow multiple free accounts for the same person.
Note that even in those cases when additional verification is requested, the email addresses are not tied to your account - we only save a cryptographic hash of your email. Due to the hash functions being one-way, we cannot derive it back from the hash: https://proton.me/support/human-verification
Of course when Proton say they don't log, we just have to take their word for it. People who don't want that element of trust can use Tor. Personally I believe their story in this case.
[1] https://proton.me/blog/climate-activist-arrest