Thank you for posting this; I too was bothered by the Lifehacker article. I have just one notebook, with 1300+ notes, and can’t see any benefit for me in having more because I don’t share any notes, I tag everything, and all my tags are organised hierarchically; I get the benefits of both tags and folders.
In my tag hierarchy I have 4 notebook equivalents, eg. “work” and “personal”, and then sub-tags under those. I’ve thought about moving everything tagged with “work” (and sub-tags) into a “work” notebook, but it seems like I wouldn’t end up with anything different to what I have now. Some notes have multiple tags, and would span multiple notebooks, so it wouldn’t make sense to drop them into any particular notebook.
I didn’t set out to have the system I have; am I “doing it right”?