I think what you’re missing is that news stories like this are designed to connect the abstract (ideas in a blog) with real people. Many/most newspaper readers are interested in other people, relationships, who is doing what, and personal connections.
The readers don’t care that there is a controversial (or radical or not) blog on the internet, they want to know if anyone important is related to the blog and whether they should try to gain influence with said people or not (by aligning or distancing themselves from said people, depending on their own connections). For example, only if the author is named can they know whether he/she is a reputable practitioner at a prestigious institution (who can thereby give influence or be vulnerable to controversy), or maybe just a random doctor in a rural town (can be safely ignored).
So for people who rely on networks of other people, such as many political, corporate, and governmental sub-cultures, the NYT gains credibility by naming names and placing people in context. In other words, the NYT is a mainstream product and service, it’s interests are perhaps not most aligned with the pseudo-anonymous world of tech and ideas that the SSC blog and HN itself appeal to and cater to.
Given that "Scott Alexander" is a semi-pseudonym, and that the "real" person behind him isn't famous, I don't see how any of what you wrote really applies. Referring to him in an article as "Scott $HIS_REAL_LAST_NAME" in the article isn't going to give anyone any more of a connection than as "Scott Alexander".
And the NYT doesn't even need to mention whether or not it's his "real" name. It's just a name. I use scare quotes because a "name" is explicitly whatever someone wants to be referred to as. The guy who writes Slate Star Codex is Scott Alexander, full stop.
I don't think tech culture is at issue here; I doubt newspapers had any issue referring to Samuel Clemens as Mark Twain back when he was alive and active.
The readers don’t care that there is a controversial (or radical or not) blog on the internet, they want to know if anyone important is related to the blog and whether they should try to gain influence with said people or not (by aligning or distancing themselves from said people, depending on their own connections). For example, only if the author is named can they know whether he/she is a reputable practitioner at a prestigious institution (who can thereby give influence or be vulnerable to controversy), or maybe just a random doctor in a rural town (can be safely ignored).
So for people who rely on networks of other people, such as many political, corporate, and governmental sub-cultures, the NYT gains credibility by naming names and placing people in context. In other words, the NYT is a mainstream product and service, it’s interests are perhaps not most aligned with the pseudo-anonymous world of tech and ideas that the SSC blog and HN itself appeal to and cater to.