the thing with having a single mesh with blendshapes is that no matter if you delete them, the fact remaining that the info from the mesh is still from each blend and this is what Maya will look at, so if the character raises a brow it still got all the info from the rest of the mesh in there so it has to look at each point.

However there is a way around it. By simpley extracting the head from the mesh and duplicating it across for your blends (however many you need)

then With the original head selected then the body combine them back together then one by one merge the verts back together. Now the trick is here to do exactly one by one because if you do it all in one go maya will reorder the point numbering and screw it all up.

But done correctly and the values remain the same, you can then put the head shapes into the Single mesh, therefore cutting down in geo for maya to look at when it deforms. If you wish you can still delete the shapes after

Jay