I see no overvoltage protection on the schematics.
If the AVR can crash or reboot with more than 5V this could be a problem specially fo Hexa during agressive fly.
If a motor or ESC become shorted during a few milliseconds before final death (the time needed to burn the wires or PCB tracks) the APM could reboot or crash as well.
Nevertheless, the AVR do have clamping diodes on all inputs, except /Reset. For this protection to work the input current must be limited to about 1 mA. I can't see any serie resistor on the schematics so i suppose that the current is limited only by the op amp output capacity (the op amp measuring the shunt voltage. This one has certainly a current capacity of 10 mA or more.
Obviously this is something to be tested to be sure, and issue a warning to the user base if the test do show a possible crash or reboot.
Olivier