The design decision for introducing overlay scrollbars is described in detail in this link: http://design.canonical.com/2011/03/introducing-overlay-scrollbars-in-unity/
Essentially the decision to use them is based on the belief that having ever present scrollbars is becoming obsolete in modern set-ups, as most scrolling actions are now performed by using gestures on touchpads, scroll wheels on mice and using touch screens, rather than clicking up and down arrows or dragging a scrollbar. Removing scrollbars will provide a small increase in available screen "real estate".
If you wish to remove the overlay scrollbars this is covered in the following question: How do I disable overlay scrollbars?