New to speedrunning in general and I prefer using a rom injected into a CIA and using 3ds homebrew to install the game onto the system as it has the most comfortable controls to me. Would this be a banned platform? Technically it is not emulation as the hardware on the 3ds has just enough of the DS to be able to natively run GBA games so it shouldn't grant any advantage.

There's no official 3DS release of SMA2, so this would count as emulation. As long as it runs the same speed or slower than original hardware it won't be banned