Notes Plus lets you create notebooks and folders, the idea being to nest your notebooks into folders.
In GoodNotes you'd have Categories and Main Categories, same difference.
In Noteshelf you can drop a notebook onto another, to create a "sub-shelf".
So, all of the above have their own way of two level nesting. To me, two levels is enough - I don't like to dig any deeper when I need a note. YMMV
About Notes Plus, I used it for about a year...
The thing is, Notes Plus turns all your handwriting into vectors. Better yet: double polylines (yes, you can write in hollow letters, pick different colours for your character outlines and their fill colour). As beautiful as your writing will look, the app works extremily slow - most likely because of all the background calculation going on.
You won't notice this on a quick review, writing stuff like "This is a test" "Hello World" "Get Milk". Just try and write a notebook of about 20 pages, add some graphics in it, import a pdf, do some markup. Then... try to select and move a sentence on one of your pages. Personally, I found it to be close to impossible. The lagging is horrible to work with.
Not only that, if I were to write fast enough (taking meeting notes!), I'd often find my scribbling to be a whole word ahead of what was actually showing on screen.