If you don't link all the files (the parent folder), three will be three problems:
Note links will be broken. Even worse, if you click a note link in Obsidian, you will create a blank note in the Recent folder (instead of the real folder).
You can't create new files in Obsidian. If you create new files in external file mangers, the new files won't be displayed in Obsidian until you open the folder again via ObsidianShell. This also means that you can't add images to a note.
Hello!
I tried to open a .md file on the Desktop, but it took a lot of time to open (every time after this).
I found many folders in the Desktop have been added to the library. I think it might be these soft links being made.
Please consider if this is a Bug, as many irrelevant files were added.