Like I said, I think you're seeing what you want to see.
Stop being offended (NSFW).
I've seen lots of things in video games (e.g. shurikens, fireballs, etc.), and in art (see tepples' post), that look similar to what's depicted. I see no "secret Nazi paraphernalia".
How do you feel about
卍PSY幽記 (Manji: Psy Yuuki) (which Yuzo KOSHIRO composed the music for), or even closer to home,
what Bionic Commando was actually about?
This is all pretty ridiculous. We're a pretty diverse bunch here (and on #nesdev), but so far I think there's pretty much universal agreement that the block layout depicted
is not offensive, nor was it ever intended to be.
So to answer your question -- which is in the Subject of this thread -- no, it is not what you think it is. It's either just a cute layout of blocks, or is intended to depict a manji (卍).
It is not a Nazi swastika. I'd link you the incredibly informative Wikipedia article on the origin of the symbol, except I'm not sure you'd actually read it, simply because the article is titled "Swastika". The symbol has an amazing (positive) history -- Hitler's use of it is just one (very negative) part of history. And while I condemn what happened during World War II like most people, I don't think the world is filled with rainbows and unicorns.
Put down your gloves, open your mind, and read about the history of something. It sounds ridiculous or cliche, I know, but broaden your horizons a bit. Mario didn't write Mein Kampf.