it is not possible to open the folders from iTunes. The only thing you can do from iTunes is copy a complete folder to your computer. This is not a limitation of Cubasis but of iTunes.
The WiFi-Server is in the app to overcome these limitations and to allow editing the folder structure of Cubasis. As Akamarko pointed out, I would recommend using the WiFi-Server (Open Audio/MIDI folder, select all files, tap delete).