I can not find the way to distinguish between folders and files drop in FireFox Ajax. Looks like there are no signs in FireFox FileAPI that can tell if this is a folder or a file.
However I see that Google docs somehow can distinguish between folders and files drop. It does not relie on extensions or file length, files without extensions are uploaded correctly, as well as 0-lenth files are uploaded with no problem.
How do I distinguish between files and folders during D&D in FF?
This blog post suggests trying to read the file and reacting to the exception that will be thrown if it is a folder.
In general: First assume the folder is a file and treat it like one, at some point things will go wrong and you can react to that.