This change allows collide_shape, intersect_shape, cast_motion and
rest_info in both 2D and 3D to ignore disabled shapes and make them
consistent with the physics simulation.
In some other cases, _cull_aabb_for_body is used and filters shapes out
internally, but whenever a physics query uses the broadphase directly
without calling _cull_aabb_for_body, disabled shapes can be returned
and need to be filtered out.