Perhaps it may not be that "hidden" because you do get an in-game map, but still, In Duke Nukem 3D, in the level "Warp Factor," the whole stage is laid out in the shape of the USS Enterprise.
Of course, you're on a ship, but it's not just that they shaped the ship like the Enterprise, but they filled out all the playable area to the whole shape. There's no real proper reason to have access to places like the nacelles, except that they wanted to make the whole place shaped like the Enterprise.
And I never noticed it until I was poking around in the level editor.
That's not a swastika, that's a Manji. An old religious symbol that the nazis too, turned it the other way around and used it for evil.
Strictly speaking they didn't "use it for evil." It's a symbol, and it symbolized an evil group of people, but the symbol itself isn't evil nor used for evil.
Also, "hooked cross" is the English name for the shape itself; swastika is only really supposed to apply specifically to the one that symbolized the Nazis. "Manji" is the name of the symbol in Japanese, which is also what they called it in manuals and Nintendo Power, presumably to help mitigate any worry people might have had about there being a swastika in the game.
And speaking of, while we all may know that the dungeons were shaped like different things, what really blows my mind is that if you look at the dungeons in an editor, the whole underworld all fits together in one map the same size and the overworld. That's REALLY impressive; because they didn't just "make shapes" but they made them in a way where they had to all fit together. And with the maps people viewed, sure, people could admire the creativity in shaping the dungeons like things, but they never saw the limits they had to work with to achieve it, which would make it all the more impressive.
Likewise the Link's Awakening underworld maps (the caves and the dungeons) all fit together within large square shapes like the overworld does. I haven't seen it all pieced together, but I do believe that they has multiple layers of maps though, so it wasn't as hard for them to make the creative shapes they used. (But maybe I'm wrong; I haven't had the opportunity to view the raw map data.)