I don't think Nintendo can detect CFWs. They simply look for titles with illegitimate title ids.
If you're really scared of a ban, uninstall any homebrew CIAs you've installed, like FBI, homebrewlauncher_loader, Luma Updater, FreeShop, etc. Using Luma's new Rosalina you can launch the new homebrew menu using a legitimate title id (so while you're running homebrew, it shows up in your Activity Log as something like Health & Safety instead. You can use some piece of shovelware instead to make it look more realistic, nobody spends hours in Health & Safety...)
Use Cthulu and you can clear your activity log. That should prevent Nintendo from detecting anything, at least for now.