If the NYT actually thinks they need to use the real name of the author of Slate Star Codex to add credibility to a story about the blog, they're delusional.
I think it's much more likely that they simply don't care about the valid personal concerns of people they write about.
That's in The Netherlands, a country with different laws and regulations for the press.
This case is specific to the United States, with its own rules and protections.
I doubt the NYT has a lot of pieces on "Declan MacManus" in their archives -- if they can just use "Elvis Costello", they could certainly stick to calling the SSC guy by the name he uses online.
I am honestly starting to think real name policies are just about hating anominity at this point.
However, if your information is revealed, don't be shocked when someone approaches you with that information because you didn't cover your tracks.
What about not revealing sources? Didn't journalists used to go to jail for that one?
Bob Woodward and Carl Bernstein, of Watergate fame, famously refused to reveal their FBI source, Deep Throat, for decades. Of course, they didn't go to jail.
This shows a lack of how journalism works. Using real names isn't to "drive clicks" and "appease advertisers." It's to add credibility to a story.
Think about it: Does a furniture business advertising in the local paper care whether the victim of a shooting is named in a piece? Sure, the owner might know the victim, but that doesn't mean the business will determine its expenditures based on names.