Even if it's deliberate, I don't see how people can complain. Google has outright blocked Breitbart for years. They prevent results from that domain from appearing at all unless you specifically force it with site: and apparently HN does the same. Politically motivated censorship and restricting "reach" is just how Silicon Valley rolls. Pre-Musk Twitter did freeze the New York Post's account and many other much worse things. It'd be a shame for Musk to be doing this deliberately, even though it seems unlikely. But that's the problem with creating a culture where that sort of behavior is tolerated, isn't it? One day it might be turned around on you.
Does the value added by sources like the NYT outweigh the negatives of being occasionally biased or outright wrong? Yes.
The only "values" that matter are the personal whims of whoever happens to own Twitter, or Google or Facebook.
What gets a website censored, in the modern corporation-dominated Internet, is going against the interests and preferences of Big Tech owners - and nothing else. Nobody with any power is bound to look out for the public interest, however defined; ICANN is perhaps the only exception that comes to mind.
We can waste our time and attention debating over which targets were more or less deserving of censorship, based on our personal ideas of public interest. But as long as Big Tech is allowed to exist in its current form, we're like powerless peasants arguing about the decisions of kings.