Looking at JetspeedResources.properties.merge:
The topnav.logo.file property points to the new image that we want to display on the JPortal site. Note that all properties relating to files are specified relative to the web application root. The images directory can be found directly under the web application root.
You could also use a logo that exists on another server with the topnav.logo.url property. The topnav.logo.file and topnav.logo.url properties are mutually exclusive, you should one or the other.
Of course you dont have to use any logo. The top navigation could be customized to use a completely different layout.