Personally I prefer the side-mounted launch bays, it makes the ship feel more 'stocky' and solid. In order to keep the design looking like a heavy battleship, if you remove the side-mounted bays you have to make the ship extremely long, which adversely effects handling and causes weapons to be less accurate (because the guns will end up being spread out over a larger area than they would with a shorter body and side-mounted bays).
The current geb has similar issues with it's weapons - due to being a very 'long' ship, the guns across the body are spread out too much and that spread reduces accuracy at even short ranges.