I assume the silencer you are referring to is the little rectangle box that is near the throttle body connected to the plastic intake hose. I believe both the 4.6 and 5.4 have the silencer. It is my understanding that this piece is only intended to help dissipate sound generated from airflow. I doubt any significant increase in horsepower will be realized with the removal of this piece.
As for ECM modification is concerned it is not necessary to make any changes. The computer will adjust accordingly.
Hope this helps.