This change has now been enacted. If you use the ADE to run Autoware.Auto, Eclipse Cyclone DDS will be used automatically.
If you run Autoware.Auto outside of the ADE, then the default ROS 2 middleware (currently Fast RTPS on ROS 2 Dashing) will be used.
You can easily change which middleware is used, both within the ADE and outside of it. See this page for instructions.