How to do backups and updates properly with full device encryption?
I don't know of any implementation for non-android devices for accessing the data, although it should be fairly easy to port / implement. For an explanation how the encryption works I recommend reading the following article:

http://nelenkov.blogspot.de/2014/10/revisiting-android-disk-encryption.html

I really doubt the Galaxy Nexus has an encrypted /system. And starting from Android 5.0 it could be almost impossible to read the data on other devices than the android device itself because parts of the key are stored in otherwise unaccessible DRM areas of the system board / SoC --- not the eMMC flash (on Qualcomm devices and possibly also Intel).