There are several things going on here:
1. GitHub uses and encourages the use of the Jekyll static site generator. This is written in Ruby and any shared Jekyll plugins will be in Ruby as well.
2. There are a lot of projects that are the code for various websites of the people/organisations running them. These tend to be liberally licensed (MIT, BSD, CC-BY, CC-BY-SA, Public Domain).
4. GitHub attracted the Ruby and Ruby on Rails communities, so there are proportionally more Ruby projects than others. Most of these tend to be licensed under liberal licenses (MIT, BSD, Public Domain).
5. The website projects do not necessarily have an explicit LICENSE/COPYING file, but specify the license in either the README/README.md file or in a HTML footer or layout file that gets pulled into the pages when the site is generated by Jekyll. Or to put it another way, do any of the websites you visit have a COPYING/LICENSE file?
6. Some projects have a LICENSE.txt or LICENSE-MIT/LICENSE-APACHE file. It is unclear if these were detected in the study.
7. There are a lot of forks of various projects -- GitHub actively encourages this. It is unclear if the number of repositories examined were the primary repositories or if it also included forks.
8. There are mirrors of other projects like Firefox and LLVM/Clang hosted on GitHub. It is unclear what proportion of projects this is from the study.
It would also be useful to show the correlation of license types to languages used.
Also, this is like studying the licenses on projects.apache.org and finding that there are no GPL/LGPL licensed projects.