I split your post into a separate discussion
I have 14k+ notes; minimal Notebooks; 100+ Tags
In some ways Notebooks and Tags are interchangeable; they're both fields in the note metadata
Tags are Evernote's primary organization tool
Notebooks have a special function; to identify notes as private/shared, offline
My preference for Tags is based on the restriction of a single Notebook assignment per note
What is your process when a note fits the criteria for multiple Notebooks?
>>I find two levels of notebook hierarchy fine
With your "subtopic" in the note title, you have three levels
If I was a Notebook user, my preference would be unlimited levels; similar to Tags