No harm will come to your phone using 2 batteries. I have used 2 or more batteries with every phone I have ever owned. As for NFC there is nothing to worry there either because the only part of the NFC system within the battery of the Galaxy Nexus is the antenna. The actual NFC chip is in our phone.
EDIT: I should also add that if your using batteries with different mAh capacities it can mess with battery % because of the way Android uses battery history for calibrating battery %. Re-calibration of the battery can help make the battery % more accurate but if you can wait it out over time the battery history does drop off the oldest recorded data after a set period of time.