This is indeed possible. Simply create the sub folder has a virtual folder and select the option to not make it visible. This will allow the folder to be accessible, but won't be listed in the directory list, making it perfectly hidden but always accessible.
I've tried to do so, but the subfolder is still visible.
I've a folder "web" which is the root folder of the FTPuser. inside this folder there's the subfolder "jobs" which shouldn't be visible. So I created this subfolder as a virtual folder and unchecked "visible in folder view" - but I still see this folder if I connect via FTP.