Nintendo Account ban affects a Nintendo Network ID registered before?

It's certainly possible that if you linked your NNID to your console and connected to Nintendo's servers with it, then Nintendo could have a record of your NNID account connected to your Switch's serial number.

If you decide to allow your modified console to go online and contact Nintendo's servers then you run a high risk of getting your console banned, and possibly your NNID too.

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There are different types of ban issued by Nintendo.

People who get caught playing multiplayer games with a modified save will get banned from that particular game.

People who modify their consoles and then connect to Nintendo's servers will get their console's certificate banned.

Along with a console ban, an NNID account ban is also possible, though apparently not usually issued by itself (as new NNID accounts are freely and easily obtained). I do not know what specific circumstances/actions provoke an NNID ban.

Advice given by people online seems to range from "don't pirate games and you won't get banned but homebrew's fine" to "don't hack your console if you don't want to get banned - you might think you're fine just running homebrew but it's only a matter of time until they catch up with you".

Only Nintendo would be able to answer with certainty, and I'm certain that they won't as it's not in their interest to reveal their inner workings.

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If you want to use your console modified (and you are within your rights to do so) then you're better off staying away from Nintendo's servers with it, because they can deny you access (and they are within their rights to do so).