Libraries has changed a lot during KiCad life cycle, not only 3D models but also schematic and footprints.
But the process is giving a better library base and all previous schematic libs and footprints are saved inside the project.
For 3D models in case of a GitHub repo, I would suggest you to make them portable as in this project
In case of a complete industrial project, 3D mechanical models are not unnecessary… They are the base to create an enclosure for the product… so I consider useful to have a local repo also of the 3D models.
I also don’t like to have to check footprint and libraries each time there is a new release, but this is a cost to pay for improvements in your libraries.
You can always have a personal repo freezed, and update only what you consider useful for your product/project.
Maurice