Mud Shot would bounce off a Dragonite. It's flying type makes MS doubly-NVE, not neutral. If you paid attention to the health bar you could easily notice a difference between losing 2hp per the boss's fast move (MS) or upwards or 20hp per fast move (DT).
Given that Dragonite handily resists every single attack of Groudon's bar Dragon Tail I would assume any time you see Dragonite in your recommended to expect it to know Mud Shot. Having said that, Dragonite trails pretty heavily far behind more optimized grass, water, and ice types.