[tsimionescu]

For the same reason you choose one font over another: the aesthetics of a text matter, especially to publishers.

Now, I should add that for an article that is specifically about language, and even has some illustrations of the meaning of these diacritics, this is almost certainly a bad choice on the NYT's part. But as a general rule, I think it is defensible.

[haskellshill]

Well, I disagree that simpler means better looking. It's akin to arguing that a commie block has better æsthetics than a gothic cathedral.