The Sony updater does encrypt USB traffic while uploading firmware, but that is optional. The problem is, the new UsbUpdater
requires an RSA signature to be sent together with the new FS image (before it was only a simple cheksum). It also first erases the target partition and
then verifies the signature of the new image. That means that once you updated the firmware, you cannot upload custom images over USB as it was posssible before with ebook.py.
However, there are other ways to get into Reader