Is there any ros node that allows to move shapes in RVIZ with a phantom omni device ?

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I'm unaware of something that provides this functionality out-of-the-box, but it would be trivial to write a node that accomplishes what you want. For example, if you use @danepowell's phantom_omni package, the driver publishes a /joint_states topic that contains the joint angles of the Omni. If you also start a robot_state_publisher as seen in his example launch file then the current geometric description of the Omni will be available via tf. All you then have to do is write a ROS node that looks up the transform from a "control" frame on the Omni (e.g. the /stylus frame) to some reference frame (e.g. the /base frame). Using this transform data, you then can correspondingly move a visualization_msgs/Marker to represent your shape.