Adding the functionality to drag and drop a folder from Windows Explorer into Workbench would be a great idea to simplify checking in a folder structure. You should post that as a new "Idea".
Though we can't do that now, there is a way to recursively check in a folder and all the other files and folders within:
We'd first select the folder in the project's data view in Workbench that will contain the folders and files to be checked in:
Next we would click the "Folder" icon to browse to the folder in the Windows file system containing the folders and files to be checked in. Make sure the top-level folder you select in the "Browse For Folder" window matches up with the folder in the "To:" field on the Check In Items window.
On the Find Files window, make sure that the "Include subfolders" checkbox is not checked. Click the "Find" button and then select all the folders within your selected "Look in" folder to be checked in. Don't worry about selecting anything at the lower level at this point. Then click "OK".
And back on the Check In Items window, make sure to check the "Recursive" checkbox at the bottom before cliicking OK.
The one limitation with this method is that if all you have is an empty folder structure with no files, this will not work. Harvest will not create the empty folder structure this way. However there is a way to write a Windows Batch Script that will traverse the folder structure and use the "hcrtpath" command line utility to create the folders inside your Harvest repository.
If the above method might accomplish what you were wanting to do can you give this a try?