I can't see any reason bus-powered would be inherently slower. Self-powered might have a faster drive in it that draws too much to be bus-powered, but the difference is the disk, not the powering mechanism.
What FreakinEurekan says is true. Only difference in performance should be the SSD or HDD inside, or the bridge controller.
That being said the J2 product from Promise did have the ability to reduce performance when bus powered to adjust the the Thunderbolt bus power available. Best performance comes when AC powered.
The J2 product is the only one that comes to mind with this capability.