I use subdirectories - a lot of them! But I still love the site maps. I'm working on one subdirectory at a time, after all. The site map not only gives me a visual view of how the pages within the subdirectory are linked, they also make it so easy to add pages. If the map-less programs have ways to add sequences, for example, I haven't found them. In CSB, I can set up my navigation links in the page layout, then just add pages where they go in the site map and the linking is there with no further mess. If I want the navigation links set up differently in, say, different levels of the pages, I just use different page layouts and then add whichever kind of page I want. On a topic's main page, I can add a list of all the pages in that section by using "create list from another sequence" - and it will even change the list as I add new pages or move current pages around.
Site maps are just so intuitive that I can't understand why other programs haven't incorporated them. The only explanation I can come up with is that they're particularly useful for visually-oriented people and, very generally speaking, people who create computer programs don't tend to be visually oriented. But that same bunch came up with Fortran flowcharts, didn't they? I still set up websites with a flowchart in my head - and the site map lets me see what I'm doing as I'm doing it. Building a site without a site map is like having to add each shape on a Fortran flowchart as a separate item on a list instead of being able to see how they interact as you write the program.