It was omitted not intentionally, but because there has been a lack of a need to implement it. The control system is not based on a physical model, it just reacts to feedback. This allows the autopilot to be put in vehicles across the entire spectrum of dynamic characteristics, and then the PID controllers can be tuned to suit the vehicle.
The ROVs that ArduSub has been designed for have direct control over yaw, if not all 6DOF, so the vehicle produces yaw torque in a different manner than multirotors. It is not strictly necessary to have counter-rotating props in an ROV like it is in a multirotor. In ArduSub, the counter-rotating pair suggestions for each frame were designed to minimize the net torques on the vehicle during normal operation; whatever net torque does arise does not have a significantly noticeable impact on the vehicle after the autopilot has dealt with it.