The England striker was back making headlines for the right reasons last night with the goal which beat Chelsea in their Champions League quarter-final first leg at Stamford Bridge.
Hughes said: "Having watched his performance last night, I am obviously pleased, because I thought he was outstanding."
However, the former United striker knows Sir Alex Ferguson has plenty in reserve.
"If Rooney is not available, then that is a positive from our point of view," said Hughes.
"But saying that, they have a lot of very good players who can come in and make and impact in his place.
"While it is good news you are not facing a world-class striker, there certainly have other talents that can cause you problems as well."