1. Import the Courtyard project from the asset store (as of 2017.03.27) (or use the attached project);
2. Open the scene;
3. Notice the buggy/empty hierarchy; no objects in the Scene and loads of errors.

Does not reproduce on Windows.
Reproduces on Mac, on both: El Capitan and Sierra
Testing regression.

Errors do not show up after closing and re-launching the project, but the problem stays.

Regression: Still unclear. Unity seems to crash when opening the scene in 5.3. I do remember this working on 5.4.4p2 (now it does not work even on that version) so it might be an asset issue. So far reproduces on 5.4:
5.4.5f1; 5.4.4p4; 5.4.2p4

Potential error:

NullReferenceException: Object reference not set to an instance of an object
UnityEditor.SceneHierarchyWindow.get_debug () (at /Users/builduser/buildslave/unity/build/Editor/Mono/SceneHierarchyWindow.cs:79)
UnityEditor.GameObjectTreeViewDataSource.InitializeMinimal () (at /Users/builduser/buildslave/unity/build/Editor/Mono/GUI/TreeView/GameObjectTreeViewDataSource.cs:301)
UnityEditor.GameObjectTreeViewDataSource.FetchData () (at /Users/builduser/buildslave/unity/build/Editor/Mono/GUI/TreeView/GameObjectTreeViewDataSource.cs:224)
UnityEditor.TreeViewDataSource.ReloadData () (at /Users/builduser/buildslave/unity/build/Editor/Mono/GUI/TreeView/TreeViewDataSource.cs:52)
UnityEditor.TreeView.ReloadData () (at /Users/builduser/buildslave/unity/build/Editor/Mono/GUI/TreeView/TreeView.cs:253)
UnityEditor.SceneHierarchyWindow.Init () (at /Users/builduser/buildslave/unity/build/Editor/Mono/SceneHierarchyWindow.cs:185)
UnityEditor.SceneHierarchyWindow.get_treeView () (at /Users/builduser/buildslave/unity/build/Editor/Mono/SceneHierarchyWindow.cs:150)
UnityEditor.SceneHierarchyWindow.OnLostFocus () (at /Users/builduser/buildslave/unity/build/Editor/Mono/SceneHierarchyWindow.cs:406)
System.Reflection.MonoMethod.Invoke (System.Object obj, BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) (at /Users/builduser/buildslave/mono/build/mcs/class/corlib/System.Reflection/MonoMethod.cs:222)
Rethrow as TargetInvocationException: Exception has been thrown by the target of an invocation.
System.Reflection.MonoMethod.Invoke (System.Object obj, BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) (at /Users/builduser/buildslave/mono/build/mcs/class/corlib/System.Reflection/MonoMethod.cs:232)
System.Reflection.MethodBase.Invoke (System.Object obj, System.Object[] parameters) (at /Users/builduser/buildslave/mono/build/mcs/class/corlib/System.Reflection/MethodBase.cs:115)
UnityEditor.HostView.Invoke (System.String methodName, System.Object obj) (at /Users/builduser/buildslave/unity/build/Editor/Mono/HostView.cs:187)
UnityEditor.HostView.Invoke (System.String methodName) (at /Users/builduser/buildslave/unity/build/Editor/Mono/HostView.cs:180)
UnityEditor.DockArea.OnDestroy () (at /Users/builduser/buildslave/unity/build/Editor/Mono/GUI/DockArea.cs:86)
UnityEditor.WindowLayout:LoadWindowLayout(String, Boolean)
UnityEditorInternal.InternalEditorUtility:LoadDefaultLayout()
UnityEditor.WindowLayout:LoadWindowLayout(String, Boolean)