>>30018553We don't know what the effects of two systems with the same seed connecting at the same time, it could be nothing, or it could be something they pursue in the future.
But if you get banned, then yes your friend will get banned too, but keep in mine the ONLY ban they did is for people playing SM early, that's what the banwave was about, they may not pursue anything else at all, they haven't in the past.
For maximum security you either use your own system transfer seed (if your current 3DS has been system transferred), or you use a spare 3DS that won't be used for online and extract its seed.
There MIGHT be a way to get your system to generate a new seed in the future, there's research being done for this but it might take a long time.
