I wanted to theme my facet links, but found that the function drupal_html_id() generates a different 'unique' ID for every facet on page refresh. Not practical for theming purposes, since you don't want that facet to change appearance when you click on them. My solution was to just copy the basic link widget to a separate module, take this function out, and replace it with a css-safe version of the link text from the $attributes array. This will generate the same ID every time, and theming can be safely done.
The attached module will give you an extra widget choice in the facet settings: 'themeable links'. It's a quick and dirty solution, but maybe it's useful or inspiring to someone.
Similar to this issue: http://drupal.org/node/1367612