You could customize the code, using your templates and overrides, for the file:
/includes/templates/templates_default/sideboxes/tpl_categories.php
and add the code in RED:
Code:
if (zen_get_product_types_to_category($box_categories_array[$i]['path']) == 3 or ($box_categories_array[$i]['top'] != 'true' and SHOW_CATEGORIES_SUBCATEGORIES_ALWAYS != 1) or $box_categories_array[$i]['count'] == 0) {
// skip if this is for the document box (==3)
// skip if this category has no active products
} else {
See if that accomplishes what you are attempting ...
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