I am the developer of this plugin and it is the most popular plugin for Retina. I always try my best so that it is supported and works with all the other popular plugins.
Smush doesn't take care of the @2x files. There are internal functions Smush could use to detect those retina files nicely and properly in order to resize them. EWWW Image Optimizer is already doing that for example. That would be really good to have Smush doing this, right now I cannot tell my users to use it unfortunately.