Ok for anybody stumbling on this thread, here is a bit of statistics on the 3D library status.
New library: https://github.com/KiCad/kicad-packages3D
Old library: https://github.com/KiCad/kicad-library/tree/master/modules/packages3d
As of yesterday (2017-10-04) there are 7101 footprints available in official footprint library (without deprecated footprints). Out of these 1835 do not have a 3D model defined.
For those that do have a 3D model definition one can find 2722 models in new library and/or 3357 models in old library.
If not for missing 39 models, one could say that new library is a subset of old. I can only humbly suggest to library maintainers that they integrate these models also in old library. This would make the relation between libraries easier to explain.
The list of missing 3D models in old library: files_in_new_not_in_old.txt (1.2 KB)
What is interesting is that 1870 footprints have a 3D model definition but there is no 3D model neither in new or old library. In the long run this should probably have to be cleaned up. I am attaching the list of footprints with missing 3D models: files_without_3d_model.txt (145.7 KB)