Is it a bad idea to have a folder and a notebook in a different folder with same name? I just realized that I have a folder and OneNote Notebook (that is located in a another folder) with the same name. Is this a bad idea? Could the filesystem mix them up?
You can easily have files (and directories) with the same name in different directories. You actually already do, even a plain macOS installation contains files/directories with the same name in different directories) (e.g. /System/Library and /Library, and then ~/Library for each user account).