We primarily use private phabricator and gitolite instances for internal stuff, but we also have OSS things in regular public GH repos. We do have a few private GH repos, but AFAIK, you're not supposed to version control internal stuff on GH, and there's no real reason to use a private GH repo, except for legal review prior to open sourcing.
I don't have any context on why someone would have put production secrets in a GH repo. If it had happened in my team, I would definitely have sounded the alarm at code review.