Personally I have not used the Due, so I can’t help you much here.
According to this Arduino post, the Arduino Due is not directly compatible with the Dynamixel Shield, because the Due uses 3.3V for its I/O pins and the Dynamixel Shield uses 5V for its I/O pins.
In the past I have used this Logic Level Shifter to interface between 3.3 V and 5 V and it worked great for me.