Notebooks, do not have to be stored in ipynb form, I would suggest to look at https://github.com/mwouts/jupytext, and notebook UI is inherently not design for multi-file and application developpement. So training humans will always be necessary.
Technically Jupyter Notebook does not even care that notebooks are files, you could save then using say postgres (https://github.com/quantopian/pgcontents) , and even sync content between notebooks.
I'm not too well informed anymore on this particular topic, but there are other folks at https://www.quansight.com/ that might be more aware, you can also ask on discourse.jupyter.org, I'm pretty sure you can find threads on those issues.
I think on the Jupyter side we could do a better job curating and exposing many tools to help with that, but there are just so many hours in the day...
I also recommend I don't like notebook from Joel Grus, https://www.youtube.com/watch?v=7jiPeIFXb6U it's a really funny talk, a lot of the points are IMHO invalid as Joel is misinformed on how things can be configured, but still a great watch.