Why do high altitude air-launch plane designers choose to use two fuselages?
It is simple to maintain symmetry if the launch vehicle is in the middle, with two fuselages on either side.

With only one fuselage, the departure of the launch vehicle would change the symmetry, and therefore the lateral stability.  

One possible exception is if the launch vehicle is directly above or below a single fuselage.  This was done with the M-21 carrying a D-21 launch vehicle, where the D-21 was directly above the centerline of the M-21.