We looked into this and found that missile drones do indeed still fire at a player executing a defensive maneuver. This is due to the lock-on functioning a bit differently than a player's lock-on. We'll get this fixed in an upcoming patch!
While you're at it, can you fix the double cluster missile bug where the second missile still hits you even if you execute an engine maneuver? This occurs when you use the maneuver AFTER the missile has been fired, it will still hit you, though if you use it before the missile has been fired it will miss as normal.