Hi @Blublub, welcome to the forum 
The Navigator isn’t set up with general purpose digital inputs, and the only digital input directly supported by the ArduSub firmware is the one for the leak sensor. The ADCs can also be used for firmware-enabled functions (like an analog leak sensor), but I don’t believe the autopilot firmware supports streaming the raw ADC values to the topside.
It may be possible to disable some of the serial ports in the firmware parameters, then run some code on the Raspberry Pi (perhaps as a BlueOS extension) that reads them and sends the state to QGC via some form of MAVLink messages.
QGC does not support arbitrary messages, so your options would be to make use of messages QGC already supports that aren’t otherwise being used by the firmware, or to modify QGC to support additional messages.