Hierarchical menus help with app discoverability by showing all the apps the system has to offer.
Can you guess under which menu is the termina/command line program is hidden? No, unless you know in advance that it's under "Accessories". I mean, why isn't it under "system" or "programming"? It's too hard to guess what the menu author(s) were thinking so it's always hard to guess where a certain program is.