Agreed, the author who writes under a pseudonym to protect himself should definitely be part of the story. We definitly talk about Scott Alexander, the pseudonumn everyone knows to be connected to the blog.

I'm not sure why though, the NYT, would need to know the name that is purposely never used.

If you really need the name sooo bad, then just don't dox him and drop the article. That's perfectly fine.

As long as they don't dox him everyone is cool.

If they can't write the article without doxxing him then they should just drop the article.

Whatever they do they shouldn't dox him. And if they can't write the article without doing so, then they shouldn't write it.