1. `System > Configuration > Advanced > Disable` Modules Output will not actually disable that module. It work as the name suggest, disable modules output.

 When you look at 

        abstract class Mage_Core_Block_Abstract


        final public function toHtml()
            Mage::dispatchEvent('core_block_abstract_to_html_before', array('block' => $this));
            if (Mage::getStoreConfig('advanced/modules_disable_output/' . $this->getModuleName())) {
                return '';
        // It is checking If its in disabled mode then just return blank output

2. While `app/etc/modules` completely disabled module