Piracy aside, can't you just buy the DSi version on a DSi and then do a system transfer to your 3DS?
I got a copy of Cave Story (DSiWare) on my 3DS that way. And I also have the 3DSware version too right next to it
I got a copy of Cave Story (DSiWare) on my 3DS that way. And I also have the 3DSware version too right next to it