Thrusters work better the further away they are from the center of mass. So with a cube design, you end up requiring a lot more thrusters for the same maneuverability. The pro's - as you mentioned - usually far outweigh this con for most people. Other potential issues might be firing arcs, especially so with the upcoming combat update and the obvious extreme vulnerability you have against hull piercing weapons but if you manage to keep your shields up, that's a non-concern.