The original forum thread outlining this issue is locked but I wanted to add a note.
If you call

EditorSceneManagement.MarkSceneDirty(game_object.scene);

immediately after updating the hide flags of game_object, the hierarchy window will update to reflect those changes. Furthermore, changing hide flags alone did not appear to mark the scene as having unsaved changes (dirty?), so this might be an appropriate workaround for the time being (this issue has been active for more than a year and seems to affect most if not all versions of Unity).

Original forum thread: https://forum.unity.com/threads/bug-g-gameobject-hideflags-hideflags-hideinhierarchy-does-nut-update-hierarchy.704078/