Deification's last ability doesn't prevent damage. All damage is still dealt to the affected planeswalkers, and any additional effects of that damage will still happen. For example, if a 3/3 creature with lifelink attacks an affected planeswalker with two loyalty counters on it, 3 damage will be dealt, causing the controller of the creature to gain 3 life and one loyalty counter to be removed from the planeswalker.