excluding ever-changing JS will most certainly be worth it, as you will have significantly less files in the autoptimize-cache-folder and it will re-use of aggregated JS/CSS in the browser cache.
regarding wp super cache or W3TC; no off the shelve solution, just pointing out that automaticallyremoving autoptimized files that are 2 days old might not be the best solution. it is something I plan to work on, but no idea how, yet.