1) Yes, you can edit layouts directly, and it works. Need more details how you tried it. And you can look into SE4 hooks (yes, more flexible and more complex way).
default.tpl:
echo $this->hooks('onRenderLayoutDefault', $this);
2) default-simple.tpl is auxiliary layout, it used for post-action messaging mostly, see Forum_TopicController::deleteAction() for example:
return $this->_forward('success', 'utility', 'core', array(
'messages' => array(Zend_Registry::get('Zend_Translate')->_('Topic deleted.')),
'layout' => 'default-simple',
'parentRedirect' => $forum->getHref(),
));