If I delete a to-do that had a linked note, does the note get deleted?

Your note on the device is not deleted — only the to-do is. The app's internal cached copy of that note's PDF becomes "orphaned" (no to-do points to it) and gets cleaned up automatically on a later sync. Any PDF you'd saved to ~/Documents/Supernote for that note stays where it is — the cleanup never touches your saved exports.