In mojoportal, modules are features that plug into the content system pages. Menus are not modules though custom modules may have their own menus. Those will be feature specific and unrelated to the main menus.
The menus in mojoportal are basically just views on the site hierarchy. The site hierarchy is the parent child relationship of pages. The Site Map page shows the actual complete hierarchy whereas menus can show parts of the hierachy starting at a certain depth and going to a specific depth. All the pages in the menu are virtual pages, that is they don't correspond to physical files. You can change the parent child relationship of pages at any time and the menu (and Site Map) automatically adapts to the current site hierarchy. So for example on this site I have a topmost menu that is horizontal, it starts at the top level of depth and only goes a single level deep so it shows just top level pages like Home, Blog, Download, Documentation, etc. If you visit the Documentation page for example, it has child pages so the next level of menu appears and it is also a horizontal menu limited to a single depth. So if you go to Documentation > Installation you see a third level menu that is vertical and it has no depth limit, it can go any number of levels deep from there as a treeview.
Some menu arangements don't look right unless you arrange the site hierarchy to fit. For example, on this site I can have maybe one more top level page then if I keep adding more it will crowd outside of my horizontal menu.
Almost all of the skins included have vertical menus but you don't see them unless there are pages deeper than 1 level because most have horizontal menus for the top level pages. If you create pages that are child pages of the top level pages the menu will appear.
Hope it helps,
Joe