Which is possible through the use of other sources. But it depends on the situation. A pseudonym is appropriate for victims of sex crimes and exploitation.
Anonymity and/or pseudonym are appropriate in certain situations. In this situation, you have a source you know which is credible (you know their name), and they ask you not to publish their name. In such a case, it is standard journalist ethics in The Netherlands to not disclose the name. Sex crimes and exploitation are two (good) examples of such, but there are other examples as well. Consider for example a whistle blower, a (former) member of a cult, or -to put it generally- someone who can, realistically, be threatened when their real name is released. Such is the very case here. I am in awe that The New York Times does not adhere to the very same principles as the Dutch media do, although I am aware that the vow has been broken here as well (such as in the case of Rob Oudkerk and Parool's Heleen van Royen).
there's nothing stopping the NYT from being more ethical than US law requires them to be. and they regularly argue that current US law isn't sufficiently ethical (though perhaps not on this issue).
This is what bothers me most about the story. If someone is "internet famous" for blogging under a particular name, but not famous at all in their private life under their real name, their blog handle is newsworthy and their real name is not. It would be like reporting on an actor or musician and insisting on using their birth name throughout the story, with one reference to their stage name at the beginning of the piece.
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.
