Well in the normal scripts operation you would not hide the navigation. You can do as you wish maybe clear the contents of the menubar template if you dont want a menu but I do not understand why you would not want a menu.
Reason is I integrated all the links into the main navigation bar on my theme. Now with the default bar I have two sets of navigation and its not needed. I did this to make it look more integrated. I have several different plugins running on site (photopost classifieds, vbadvanced dynamics, ect) and it looks cluttered having a bunch of different navigation bars all over the place.