I don’t really fault the NYT for writing Hanoi and Vietnam, not Hà Nội and Việt Nam. It’s a newspaper for English-speakers, at the end of the day. It calls Warszawa Warsaw, Praha Prague, Москва Moscow, and hundreds of other places by their English names.
I wouldn't expect Russian newspapers to write New York instead of Нью-Йорк, either.
Nguyễn Phan Quế Mai is the one name that the NYT did not strip the diacritics from. Every other Vietnamese term and name has been stripped (including the names of the other authors in the reading list), but the article author's name, alone, retains its diacritics in the NYT article. They do seem to have gotten the diacritics subtly wrong in the article subtitle vs. the byline (which is correct and, I assume, generated automatically).
I wouldn't expect Russian newspapers to write New York instead of Нью-Йорк, either.