One of the great things about javascript based analytics is that the cached version of your page is just as good as someone grabbing it directly. You can set long cache times on all of your pages without worrying about people viewing your site without you knowing. This more than counteracts the handful of people who have javascript turned off.

This is also particularly important for sites like heroku who have an HTML cache sitting in front of your site. If you serve pages that are cached, javascript logging is your only option.