Help menus added to an application do not replace the standard Apple help menu. There now appear to be two help menus,
Help Menu 1: added via Qt; includes system Spotlight search widget
Help Menu 2: seems to be automatically added by OSX, includes one item - help for the application.
The correct behaviour should probably be for the second menu not to be shown.
To reproduce this you need to set up an application bundle with help book specified in the main bundle property list, i.e. set the CFBundleHelpBookFolder and CFBundleHelpBookName keys.
The attached example shows one help menu under Qt 5.5 but two help menus under Qt 5.7.1
Could be related to https://bugreports.qt.io/browse/QTBUG-43750