As @PeterT said, the KoboTouch driver uses the database on the device to see books. Anything not in the database is invisible to the driver. That is because if the books are not in the database, then nickel, the software supplied with the device, does not know about them. If you are bypassing nickel, then the KoboTouch driver will not find any books on the device.
If you don't want to use nickel, then don't use the KoboTouch driver. Disable it and either use the "Folder Device Interface" driver or the "User Defined USB" driver. Both of these will treat the device as basic USBMSD and scan the filesystem for books.
This information should be somewhere in the KOReader documentation. I don't use it, so I've never looked.
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