What a long discussion... been going on for years. There's clearly a user desire for nested Notebooks beyond the current 2 levels. And there's clearly technical reasons Evernote can't offer the feature. Stalemate!
Tags can work as a substitute, but require rigorous maintenance. You can't just create a tag off the top of your head and... forget it. Do that often enough, you won't find your special tree in the forest.
My solution is to use the Stacks and Notebooks for Big Topic areas. Then I use tags to emulate the menu structure below the Notebook level.
I have two gigantic tag hierarchies:
My business tags are all A-Z alphanumeric: A0000 to (theoretically) Z0000. So... > C0600 Insurance > C0603 Medical.
Non-business tags start numeric: 1...99. So... > 20 Investments > 21 Software setup.
It takes some discipline to keep it clean, but it's all I can do to keep thousands of Notes from getting lost.
I'd still like to see nested folders, which would simplify the vast number and rigid structure of my tag system.