Similar to the change I made to the blosxom categorylist plugin, I modified b2evolution's category list module to only list a category if there are posts in that category. I also inserted a space between the checkbox and the category item.
This change goes in the file: {YOUR_BLOG_ROOT_DIRECTORY}/skins/_categories.php
Here's a running tally of the diffs.
And here's my post on the b2evolution forums about this.