I have also activated the Menu Plus add-on but I still can not see the “Navigation Logo Upload Box”. Im using the newest version of generatepress theme 2.3.2 and gp premium plugin 1.8.3.
the latest version of GP changed the way this works. Now you simply add your logo in the site identity and check the Navigation as Header option in the Customizer > Layout > Header.
thanks for the feedback I have found the new place.
In my old website the logo option is still in the old place, but this should not concern me I guess, as long as the logo is in the right place ^^