Not to be confused with twin fuselage design. Especially for high wing span UAVs, twin boom design seems to be a better option as it will reduce wing bending in flight. But it is not normally used, are there any aerodynamic(or otherwise) disadvantage of this design?
The main disadvantage is flutter. The booms add a mass behind the axis of elasticity which will twist the wing when it bends. This twisting will increase the local angle of attack when the wing bends upwards and increases the bending moment, and vice versa on downward deflection. Once the plane flies fast enough, flutter is hard to avoid. The main remedy is to make the inner wing stiffer in bending and torsion, so the flutter frequency is shifted outside of the flight envelope. This costs weight, though.