Hi,
You may need to delete the urls from Administration > Advanced Tools > Url Manager if you want to be able to re-use them. You may also need to look for them in the Advanced Tools > 301 Redirect Manager and delete them there if they are redirecting. These redirects would be created if the name of the page were changed, it would change the url and a redirect from the old url to the new one would be created.
Pages are not physical files, all the pages in the menu are served by /Default.aspx?pageid=x the friendly urls for those pages all are re-written to /Default.aspx?pageid=x but the frindly url is shown in the browser.
You might find it helpful to watch part 7 and part 8 of the developer screen casts, as it explains concepts about mojoPortal and how it works.
http://www.mojoportal.com/developertrainingvideos.aspx
Hope it helps,
Joe