theme_boxes_box() is called for every box, though it's in admin.inc

theme_boxes_box() is in boxes.admin.inc, which implies:

a) it's only for admin pages
b) it's a function that is not often used, hence allowing the admin.inc file to only be loaded when necessary.

However, boxes_block_view() calls this for every box:

    $block['content'] = theme('boxes_box', array('block' => $block));
    $block['boxes_plugin'] = $box->plugin_key;
    return $block;
  }
}

This means the whole of boxes.admin.inc is loaded whenever a box is displayed. Which makes the use of a .inc file fairly useless.