First, to be clear, you can use multiple emuNAND setups. If you have a patched system and you care about online play, then you are going to need the following:
- Your sysNAND forever trapped on 4.1.0 for accessing PegaScape
- A clean emuNAND for online play on 8.1.0
- A dirty emuNAND on 8.1.0 for hacks, kept offline (or with 90DNS and/or Incognito installed)
Some would argue that your sysNAND is technically dirty because of Fake News, but it can easily be removed, and in principle, it won't leave any traces behind. I also don't think anyone has been banned yet for having Fake News installed.
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Using an emuNAND is recommended if you're habitually using homebrew and you also care about online play. Only using Atmosphere and certain homebrew (offline) is less likely to get you banned than installing NSP files, however.
There is still a ban risk, even though it's much lower than installing NSP files. If you're going to habitually use homebrew, and you care about using online play, I recommend using an emuNAND.