They definitely won't look as good as updated apps.
Good news is that any developer with a head on their shoulders should have been prepared well in advance with retina dpi images for their iPad apps.
First, it's obvious looking at the iPhone that it was at least a future possibility, and second it's been rumored specifically to come to the iPad since the lead up to the iPad 2 launch.
I bet that lots and lots of major apps will be updated to retina quality as soon as their updates go through the approval process.