Separate/different sharing of sub-folders in Notes.app
Yes you are right. You can share folders or individual notes in the Notes App. But you cannot share subfolders individually.

After some testing I found the same issue as you:
When you give person Y access to a subfolder, the whole parent folder with all notes and subfolders will be shared. When you try to remove access for Y from a subfolder, the access to the parent folder and all its content and subfolders will be removed. This is not a clever implementation, I have to admit.

The only solution using the Notes App for this purpose is to convert your subfolders to top level folders and set privileges individually for each folder and collaborator.

Unlike I previously described, you can set privileges on a per user basis to read only or write. But the implementation seems not intuitive at first glance, since the access right dropdown appears first on the folder/file level. As soon as you set different privileges for different collaborators, this dropdown changes the the new option "mixed privileges".