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.
Ah, I see you're from a different culture to me. I gave up reading anything that looks like mainstream news, and am much happier for it, in part because I wholeheartedly disagree with the mainstream news's founding sentiment which you summarise as "and that's important".
The story is about the blog, yes, but a portion deals with the _person_ or _people_ behind it. And that's important.