Full page caching, using APC or disk-enhanced, doesn't alter any part of the page. For that, there are other options, such as minify. Also, W3TC or any other caching plugin has no control over javascripts that are loaded from external domain/s.
If a page loads faster, due to caching, it is only going to increase the time spent by the visitors on that page. But, if a page loads slower, that only frustrates the visitors who are likely to spend less time.