I've got a resource creating directories/subdirectories full of images, which are directly uploaded to the server.
The aim is to avoid album's and images' automatic generation. (but not for thumbnails)
Could you give me some advices and which functions do this job ?
Zenphoto is file system based and will generate these if discovered automatically if image theme functions are called.
If you don't want them to be displayed on your site initially itself you can default there publish status to be unpublished. There is a utility button on the admin overview pages for that.