DSiWare CIAs don't have exefs/romfs files inside them, theyre literally DSiWare NDS files packed into a compressed file. To extract files, you'll need software compatible with NDS files, such as Tinke.
Sorry to bump, but has anyone found the cause of why the server software is not sending C-Stick, ZL or ZR inputs to vJoy? I'm trying to use my broken old N3DS as a wireless gamepad and I can't play my game without a right analog stick.