Hmm, I installed version 1.1's CIA onto my N3DS and it runs really well! The music isn't playing, and I am absolutely certain I downloaded the BGM-version. One thing I would like to know is if the changing geometry from the original is going possible in the future. Like how in the Android/PC versions, the shape of the hexagon changes based on how long you have been playing to increase the difficulty. If this is already implemented and I just didn't play long enough to see it, oops.
Regardless, this is awesome! I've always thought that the 3DS would be a perfect fit for Super Hexagon, especially after the developer ported VVVVVV to the system. I always expected an official port with 3D and all kinds of crazy vfx happening, but nothing ever happened. That is, until now! Awesome work, dude! Hope to see this mature in the future!