Ocarina of Time 3DS (60 MB) is almost double the size of Ocarina of Time N64 (32MB). Wonder why that is. That orchestral track probably took up a lot of space but I'm sure they have some sophisticated compression routines nowadays. Honestly can't think of what could account for all the extra space.
I'm not one of those tech guys but OoT 3D has more inputs thanks to the addition of the touch screen. It has better music (which you mentioned) and the textures are much more detailed despite managing to maintain the nostalgic look of the original. I has the extra mode added for when you beat the original, too.
That's my best guess, anyway. I'm normally wrong about these things, though.