I keep getting errors from google bot saying the wp-minify js and css files dont exist. Its because this plugin constantly keeps changing their names when it goes about refreshing the content (or i modify the content). Because of that i could imagine search engine bots would penalize for the constant problems occuring on the site (dead js/css files).
So i think you should have an option to keep file names the same (and allow the user to provide the names ideally). So when you refresh and rebuild there is always the same file name there.