Interesting observation, but maybe it is just a coincidence since I am not aware these numbers appearing anywhere? Found this reddit thread that talks about same thing.
Here’s an interview with controller′s designer that explains the meaning behind symbols. I think number theory is just a coincidence since I think it would be mentioned in this interview as well.
Other game companies at the time assigned alphabet letters or colors to the buttons. We wanted something simple to remember, which is why we went with icons or symbols, and I came up with the triangle-circle-X-square combination immediately afterward. I gave each symbol a meaning and a color. The triangle refers to viewpoint; I had it represent one’s head or direction and made it green. Square refers to a piece of paper; I had it represent menus or documents and made it pink. The circle and X represent ‘yes’ or ‘no’ decision-making and I made them red and blue respectively. People thought those colors were mixed up, and I had to reinforce to management that that’s what I wanted.