Depends if you installed pirated games and CFW on the Switch already.
Even if you delete pirated games, some traces remain and you will likely get a ban.
If your Switch is 'clean' then it should be no problem.
Yes you can use emunand for cfw only and sysnand for legit stuff.
But only if your sysnand is not dirty and you haven't installed anything sketchy on it. If you did, then look for a way to clean your sysnand beforehand.