Ex-England international Rooney spent 13 years with United, before departing for Everton in the summer as the Red Devils' all-time leading goalscorer.
The 31-year-old will make his first return to the Theatre of Dreams as an opposition player when the Toffees take on the league leaders next Sunday, aiming to get back on track after defeat to Tottenham Hotspur last time out.
Writing in his weekly One Hour Behind blog, Mata said: "They've just suffered a tough defeat against Tottenham, but they have made very good signings and of course they have a player like Wayne Rooney.
"I hope Old Trafford will welcome him as he deserves. It will be weird to see Wayne playing with a different shirt, to be honest, but this is the decision he made last summer and we wish him the best of luck."
Rooney has two goals and an assist in his eight matches since returning to boyhood club Everton.