When it comes to 2D, they use software like Live2D (supported by Ren'Py), as for 3D, they use Blender/DAZ, or a mixture of both. 99% don't do anything within Ren'Py, there are some experimental shaders were you can bring life to scenes by using wave maps, but I doubt any game seriously uses that. Either way those wouldn't be interactive, and the options I mentioned are easier and faster to do.