This has been requested earlier. The problem is, when you drop folders into a HTML upload form, it adds the FILES and ignores the folders (because technically, it will never upload a folder, just the files inside). It might be possible to detect the PATH of the local file, to calculate folders that must be created on server ... So even if this might work, we would then need to CREATE folders on server from the upload PHP script, while files are getting uploaded.
Currently, the uploader will upload all files to the dir selected. It will not upload and automatically create folders in the structure that you dropped folders into the upload.
I will add this as a request, as it might be possible in a future release.