Nintendo could check for headers and they will be most likely removed, 0ed or if thousands use the same highly suspiciousBut what about homebrew usage in emunand, or even running CFW within emunand. That doesn't sound ban safe either. Plus I dont see how games in SX-OS can be detected when they're legit titles that show up as cartridge games. It wouldn't register as an unauthorized software.
Edit: Oh you mean keeping emunand offline, I see now