Yes it matters which pulley is on top...specifically for shimano. The top pulley has some side-to-side play purposely engineered into it as has been mentioned. The bottom pulley does not typically have any side-to-side play. If you swap them around you will probably experience a decrease in shifting performance or become super frustrated with not being able to dial your rear derailleur in consistently.

After market sealed bearing pulleys (top and bottom) tend to not have any play in them. Some folks have had great success with them and others have sworn them off.

I would recommend finding any pulley that is compatible with your derailleur model made/marketed by its manufacturer. If you have dura-ace there is no specific need to use the really expensive dura-ace pulleys with the bearings in them as you probably would not notice any decrease in performance from shimano's less expensive pulleys with bushings.

The plus to the dura-ace pulleys is that they make your wallet lighter which can amount to significant gains when climbing those steep hills if you use your wallet to help create an aerodynamic hump in your jersey pocket.

YMMV
-j