This touches on the much broader issue, which is where I think some confusion still lies. 

In Masterpages, your logic (business and presentation) lives with the page: whether that is a master page or a child page.  If you wish to change behavior you must go to the code, wherever that code lives, and make the change.

In DotNetNuke, your logic lives with the module and or skin objects.  Modules and skin objects are designed to be re-useable components which encapsulate a set of logic, but which, like all good components, expose a set of properties that allow you to customize the behavior at runtime.  So in the DotNetNuke world we do not require a programmer to make a change like updating a link or changing the look of the website - these can be done by admins and designers.  In DotNetNuke, programmers focus on creating components (whether modules or skin-objects), and don't worry so much about the visual or content side of the site.  What this means is that the site can be maintained by content owners rather than a bunch of developers.

What this means in a practical sense is that items like navigation become an issue of finding the right navigation components and placing them in the skin or in a content page (depending on whether it is a skin object or a module).  These objects then treat your navigational elements as just one more type of content that can be maintained by the content owner.  In many cases these components are smart enough to link to other content in an abstract manner, such that when you move a page on a website from one area of the site to another, the links still work.