GitHub is just a wrapper web service over Git technology. Just like any other version control system, Git stores your committed files under a directory on the server like github/users/username/repositoryname . Under this directory there are the most updated files which are exact copy of your local clone.

Does Git store deltas or whole files?

Git does use deltas for storage.

Not only that, but it's more efficient in it than any other system.

How is Git repository data stored?

Within a repository, Git maintains two primary data structures, the object store and the index. All of this repository data is stored at the root of your working directory in a hidden subdirectory named . git.