The object will not be saved to the Scene. It will not be destroyed when a new Scene is loaded. It is a shortcut for HideFlags.DontSaveInBuild | HideFlags.DontSaveInEditor | HideFlags.DontUnloadUnusedAsset.
You must manually apply the flag to the entire hierarchy of game objects you desire to affect. For Prefab instances in a scene, you can set the hideflag on the Prefab instance handle object as a way to set the same hideflags on all the objects of the Prefab instance. (See PrefabUtility.GetPrefabInstanceHandle).