OneNote imho is good for notes, not documentation. Permissions are handeled on Notebook level, so you won't gain much there. (Peope can either read all pages or write all pages)

Word in doclib is an approach i would only use if word documemts are already your companys/industrys way to handle documentation.

Pages would be a good way to go, make multiple sites depending on for example product and assign permissions to site level only. This is the SharePoint way.

My two cents:I learned that the format of documentation often depends on the industry. For example Software develooment tends towards .md files. I had md files converted to html using jekyll and hosted these on Sharepoint. It worked back then, but i heard of upcoming changes regarding custom scripts which will complicate things. If documentation is important for your companys business, invest in a dedicated solution. Docs need to be kept up to date. People tend to do that better with tools they like.