Maybe you mean it's done with OpenGL, so _hopefully_, _if_ you happen to have the right graphics card with the right driver, it _may_ be done in the GPU.
But how can this be related? Are you, MisterIO, showing all the 100 windows at the same time? Or maybe is GNOME Shell so dumb as to try to show all those scaled-down windows at the same time? Or worse, is it drawing them even if they are not shown?