This one was curious. The ClickToFlash Settings were only in the Safari sub-menu if I first visited a site and opened them through the grey gear. They were also temporary. If I closed Safari and re-opened it, the ClickToFlash Settings were no longer in the sub-menu.
The apparent temporariness of Safari's ClickToFlash Settings menu item is because it's 'contextual': it only appears on pages with Flash [placeholders], at least initially in a Safari session.
