>>350624746
That's the eternal battle brah. 
For absolute performance check out unity performance guides; it's still generic unity. 
tl;dr reduce material and mesh count. Don't run shapekeys on high vert count meshes (seperate face mesh good because face shapekeys are running all the time)
It's all a balance though. If the toggle is only a small number of verts, then it would be okay to do shapekeys. If it's a large number then you definitely want to toggle a mesh.