All roms should work online if you are using WAIO or WoodR4, even YSMenu with latest patch, Pokemon Black does work, and I can fully do a Game Sync and battle online. So if you have an R4 use WoodR4, if you have a clone like N5 use WAIO.
Your friend is totally wrong, if Nintendo wants to bust every flashcart user, then they will stay busting for 10 years, think of it logically.