When our space company was looking at lifting bodies and winged vehicles on top of conventional rockets, the main issue was control during the atmospheric portion of the launch. An assymetric aerodynamic load like that on the top of a rocket is not a simple issue.

Note that the X-37 is launched inside a large fairing, although security is probably another factor there.

It may be possible to link the aerodynamic control surfaces of the spaceplane to the guidance system so it can help instead of hinder. That kind of thing is over my pay grade.

I do know that the only design I worked on that put a small spaceplane on a conventional rocket eventually ended up with it mounted on the rocket's side (it wasn't multiple-staged). I still have the tradeoffs on file somewhere.