Trophies are linked to your PSN ID, unless you have changed your user name they should appear when you look in trophies.
Did you backup your data from the old PS3 and put it on the new?
You need the Wipeout game save data from your old console to be put on the new one to have everything back the way it was, otherwise the game will treat you as a new player and you will have to play through again to open everything up.