I found out how to - select a bookmarked destination, and to - start/stop navigation but I am still looking for a way to - toggle 2D/3D with dbus. It would be nice if someone who knows how this can be done would post this here.
dbus-send --print-reply --session --dest=org.navit_project.navit /org/navit_project/navit/default_navit org.navit_project.navit.navit.set_attr string:"pitch" variant:int32:30