Best method is to log in through ssh and issue the "halt" command, wait for a few minutes for things to cool down.
This way you give the psu time to cool down and most important the filesystem on the sd card is unmounted.
If you just flip the power switch under full load chances are that you get a power spike on the 12 volt rail and damage the mounted filesystem.
I looked around their system image pretty carefully and I couldn't find anything that was writing to the SD. Yes, its mounted, but it should still be idle and consistent. It is possible I missed something, but I don't think so.
Reducing the power load to a minimum before physically powering it down might be more important.