Yes, WP Super Edit will make some database calls outside of the editor.
WP Super Edit is designed to include files that may be related to the tinymce plugins that you may have installed or created. WP Super Edit has to find out what tinymce plugins you have activated to execute any function that may be related to that tinymce plugin.
I use this myself to produce things like a home grown TinyMCE button that inserts shortcode for some internal functions on a client site. The WP Smilies WP Super Edit tinyMCE plugin is an example. Once that TinyMCE plugin is activated in WP Super Edit, the shortcode functions to make WordPress smilies IMG tags will get activated.
So the database has to be queried, the plugin shortcode functions have to be loaded or your visitors would not see the smiley image on the published document. This is just an example, I could bore you more with some of the custom things I've had to create for people :).
I'm working on a few other things with WP Super Edit at the moment, and I am rethinking some of this functionality. I may just trash some of the includes functionality and move to setting up hooks instead. It may be more appropriate to move the custom work to separate dependent plugins.