So Ndru fires a cluster missile...... do they STILL both get an extra die, or does only ONE of them get an extra die?
Both attacks get the extra die. Resolving abilities that increase or decrease the number of dice is part of the "Roll Attack Dice" step, which will still happen for each of the Cluster Missile attacks. Since N'dru's ability isn't limited to once per turn, it will still happen on every attack roll.