To make this work, you'd have to modify the Smarter Navigation plugin to use AJAX for generating the links, as hinted in the WP Super Cache FAQ (the "How do I make certain parts of the page stay dynamic?" question).
I am not sure if that can be done, while still maintaining the performance that WP Super Cache brings in the first place. Full-page caching (the same output for all users) is fundamentally at odds with personalization (different output for each user).
The next-best solution would be to use object-caching, provided by W3 Total Cache, Memcached Object Cache etc.