This is a convenient way to upgrade, and is certainly a good thing for development / testing environments. On a busy site there might be a slim risk this technique could be problematic. Although the file system is updated in an atomic transaction, a web browser could still read from both the old and new versions of the site.
Also a resource removed by the "next" release, may result in an HTTP 404 error. Whether that actually breaks anything depends entirely how your website works though.