Apple has a design philosophy of reducing cords with their own products. Hence the ADC connector on displays, elliminating a power cord going to the monitor. Same theory with the Apple Pro speakers.
With the G4 Cube, they were USB based, but needed more power then the normal USB specification. So the USB ports in the Cube can put out more power then normal.
Now they use a seperate jack to avoid confusion, as I am sure Apple support got swamped with calls like "Why won'y my speakers work when plugged into my USB Hub/Keyboard?"