Your console cert and serial can get banned, so i think linking an account to a banned console (if that is possible) would probably ban the account too.
Overall, never use online with games that you do not own. Even if you're not doing anything online, you will be banned regardless. Only use SX Pro while in airplane mode/having your connection settings all deleted and clear your logs if you do not want to be banned. Nintendo's being crazily rigid about anti-piracy lately.
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I do believe every action you do on your Switch generates a log of some sort - so Nintendo would definetly know if you were using something that isn't normally accessible by normal means. Just in case, never go online while using anything homebrew-y, regardless of what it is. The chances of ban are really high, and they are really looking out for any chance to ban anyone.