Yes, those pin numbers are associated to the actual pins connected to the individual sensors on the Zumo reflectance sensor array, but those pins are used as digital pins, not a combination of analog and digital pins.
You are also correct about needing to cut the traces for pins A0, A2, and A3 on the sensor array and removing those pin numbers from sensorPins to free up those I/O lines. Just in case you have not already seen it, the “Adding a Zumo reflectance sensor array (optional)” section in the Pololu Zumo Shield for Arduino User’s Guide discusses the process of how to disable and remap sensors.