xping: As you list having a Kobo Aura HD, I can say what it does.
Calibre doesn't scan the drive. It reads the devices database. Then the driver checks if this books exist on the device. If there are books on the file system that are not in the device database, calibre will not report them as on the device.
When the Kobo devices re disconnected, they scan the drive and the SD card for books. Any hidden directories are not scanned. So, putting other books in a directory starting with a dot, should hide them from the device. I know people who are using the alternative reader applications are doing this.
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