This is a great plugin that I've been using for years.
There's probably good reasons why they're not, but it would be useful if that could be.
There are two problem files that I could find:
The problem line in core.php is:
I guess the conditional comment is a problem for enqueuing the suckerfish script, but this post (http://kuttler.eu/post/wordpress-style-version-conditional-comments/) seems to suggest its possible for enqueue_styles, so something similar might work for enqueue_scripts. I found that as a Resource link near the bottom of the WordPress wp_enqueue_style function reference page.
Not sure why the scripts\superfish_settings.js.php file can't be linked to in a script src attribute rather than being pushed directly into the page. If that was done then it could be enqueued properly.