It's a really bad look either way. If they did, they are currently screaming from the rooftops things best never even uttered quietly. If they didn't, they have editors who are incompetent enough to miss an obvious major issue on an epically badly timed date. No matter which it is, the NYT is taking a major hit to credibility.
I don't believe it was intentional, if for no other reason than it's really really hard to build crossword puzzles in the first place, much less build them trying to create a specific pattern in the negative space. It's also more of a spiral and you have to fudge a bit to get the swastika in there.
BUT because humans associate so easily, and they mentally create alignments from very little input, that is a really unfortunate design. Mrs. Beebo -- without any prompting or clues from the context -- saw the swastika implications from across the room.
Me: "Hey, look at this crossword puzzle that the NY Times published."
Her (face frozen in shock): Oh my god! How could they NOT see that?
And on Hanukkah, too? Oh yeah, I put this down as a catastrophic editorial oversight.