The main reason for json, I believe, is that the Jupyter client is separate from the backend. It's actually pretty trivial to run the engine on a beefy box while interacting on a light laptop (on the same subnet). With Jupyter Lab and some fiddling, you can put the server anywhere.

It's also trivial to export notebooks to .py files.

That said, my goodness do notebooks wreak havoc on git. I hope this in particular gets fixed as popularity grows.