1. `System > Configuration > Advanced` only disbaled the output of a module while still including the code of that Module in the shop

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