Thank you for your post!
I'm going to move this thread from the FileMaker Community Feedback Space (which is specifically for input on the Community itself) to the Discussions Space where you should receive more views and potentially more feedback on this topic!
Hide the menus. Create your own menu set for WebDirect using the button bar object inside of a top navigation part.
That way you only have to hide the menus as part of your startup script:
If [ get(systemplatform) = 4 ]
If it is a massive system, then it may just be easier to take this approach for the desktop as well. That way you will just need to add the top navigation part and button bar to the layouts, rather than duplicating all of the layouts and setting up all of the split navigation for WebDirect.
This question has already been brought up before as well:
I also added this to Product Ideas as a feature request, I tagged you in it so you can edit/add details as you need, but it's a pretty straightforward request.
This is our method (was used in IWP before as well). Hide those menus and make sure to include the functions needed for WD as buttons, links and other "web" objects. These can take "Hide object when" as well now.