Well, you didn’t answer my questions so I can only guess.
You are not removing by using CSS display none, but are emptying this Admin → Settings → Basic Setup input ?
top menu
Determine which items appear in the homepage navigation, and in what order. Example latest|new|unread|categories|top|read|posted|bookmarks
This being empty is not really a Bug as it isn’t normal to have no navigation.
But I think it might be a good idea to force it to have at least one. Or if not that, maybe include a Warning in the copy.
TBH I don’t know how many Warnings Discourse should have. It could make things quite noisy to have a lot of “if you do this weird unusual thing there will be breakage” warnings all over the place.