There's another angle here as well: I doubt NYT editors are familiar with Vietnamese spelling. If there are errors in the diacritics, they will not be able to spot them, and may end up with a text that appears more precise than it actually is. If they just remove all diacritics, no reader will be confused they avoid this potential for errors altogether.
"We need to remove information from the text because perhaps the author (who clearly speaks Vietnamese) may have made a mistake". Do you also think that we should remove all algebraic symbols from mathematics papers, because perhaps the author has made a mistake, and the audience may contain people that won't spot it?
