After some test, I found that I can load all classes and properties in the vocabulary if I start from scratch.
As long as I try to update the existing partial schema.org vocabulary with the full vocabulary file, I get no update and Omeka S says “nothing to update”.
If I start with a completely new vocabulary, I get all classes and properties, as in your case.
So, it looks that the update process doesn’t work.
Anyway, for me it’s ok to load from scratch but I wonder if I can replace the old schema vocabulary with this new one without loosing the existing resource templates, items and item sets that use that old version: what does it happens if I remove the old schema vocabulary and I load it from scratch?