Sounds like the Bible, which has 66 books, about 20 chapter average per book, and about 30 verses per chapter. Regardless of what your content is, do a search for Bible here and that should turn up instances of people who have the entire Bible in one TiddlyWiki, divided by book and chapter, to see how they organized what they did.
Comments:
1. Is it necessary to create them all at the outset, rather than create them as you take notes on them? I don't see the value in that.
2. You could create a manual list of tiddlers for the next section you plan to read, say 4.6 (with content of
* 4.6.1
*4.6.2, etc),
then when you are ready to take notes on 4.6.1, select it and transcludify it. Then open the link. That way there are no missing tiddlers or existing tiddlers before you are ready to add content to them.
3. Or you could create the subsection tiddlers one by one and have them backlink to the section.
4. You may consider using initial zeroes. 09.04.18, so they line up in order in the All tab and the search results.
5. Consider the Freelinks plugin. Tiddlers with unlinked references to other tiddler titles appear automatically as links.
6. You can add a chapter field to the chapter tiddlers, a section field to the section tiddlers, and a subsection field to the subsection tiddlers, to limit searches in AdvancedSearch or in list-searches (see the ListSearchPlugin) [has:field[subsection]], etc