How do Zenyatta and Mercy's damage boosts stack?

They stack multiplicatively.

From a Reddit thread, where they did some experiments:

Orb Of Discord Stacking: Confirmed! Not only that, it stacks multiplicatively! This means that orb of discord's 50% damage increase is multiplied by the 130% damage of the boost! This means that we get a damage multiplier of: 1.3 * 1.5 = 1.95 times the damage! If the orb of discord were additive (like with multiple Mercy beams), it would only be 1.8 times the damage. That's almost DOUBLE the damage! This is pretty powerful stuff!