There are several ways to handle mobile devices and doing it inside of single theme is builky and hard to maintain (as for me at least). More commonly this seems to be accomplished with separate templates or separate mobile-specific theme.
I don’t know about WP Super Cache specifics because I hadn’t used it extensively.
Plugin I currently use is W3 Total Cache. It allows you to create groups of user agents strings, for which visitors can be redirected to another theme or domain and (as I understand from description of settings) will have separate versions of cached pages.