Running XF 1.0.4 I have an add-on installed & configured. That add-on includes a Route Prefix (eg: mySite.com/myPage). There is also a Code Event Listener to add a new navbar link.
Everything works fine when the add-on is enabled but when the add-on is disabled in the ACP (it shows as unchecked, name is greyed out, and is shown with a strike-thru) the listener is disabled as expected so the navbar link does not show but going to the URL directly still serves the page instead of showing the 'page not found' error as expected. It appears then that the route prefix is still enabled even though the add-on is disabled.
I tried as both an admin account and as a guest and got the same results.
I tried with two different add-ons that include route prefixes and got the same results with both.