For clarity, this isn't necessarily a limitation on GitHub itself so much as how git itself handles files and folders.
I suppose a reamde file could do the trick, but if all you want is to assure a folder is present then it might be a bit much. Another approach I've sometimes seen people do is add a .keep file to the folder, which is just a text file that serves no other purpose than to give the git client something to include for that folder in a commit. It could be empty, or it could hold information as to why it needs to be kept around.
