i think:
your database set the limitation for resources, not MODx. But thats only my opinion, i dont know exactly...
I would put all the data, in this case, your articles into a custom-table, not into resources, if you plan to have a LOT of them.
chapters, subchapters could be resources. Then have a table with all the articles and a resource_id, which points to the chapters or subchapters - resource.
much like this:
https://docs.modx.com/extras/revo/migxdb/migxdb.tutorials/migxdb.create-a-basic-gallery-management-from-scratch-with-migxdb/
articles instead of images in your case.
Which Extras are you talking about?
You would still use pdoMenu or wayfinder for the navigation, instead of getResources for the articles, you would use migxLoopCollection.
To manage the articles, this is possible with a MIGXdb - TV, or with a MIGXdb - CMP, or both in Combination.
you can have MIGX - TV-fields also inside a MIGXdb - TV or CMP, or could also be another MIGXdb - TV and another related custom-table instead of the MIGX-field.