If the folders (or lack of folders) don’t have any meaning, I’d choose to keep a cleaner view with just “Shortest Path”. I actually use Tiago Forte’s PARA where folders do matter, but I still just use Shortest Path. When moving notes around between folders, the links keep working, or update properly, so that isn’t an issue.
Otherwise, Rishi makes an excellent point about fitting with the requirements of your other apps.