EngineSubsystem Deinitialize is not being called

UEngineSubsystem::Deinitialize()

is not called when closing the editor

In addition, (tested only with released 4.24.1) 
when recompiling a module using the "Modules" window in the editor
the deinitialize function is being called, but at a wrong order (imho)

IModuleInterface::ShutdownModule()
UEngineSubsystem::Deinitialize()
IModuleInterface::StartupModule()
UEngineSubsystem::Initialize(...)

I would expect Deinitialize function to be executed before ShutdownModule

Have a class that implments UEngineSubsystem in your module.
start the editor, and then close it.

UEngineSubsystem::Deinitialize()

is not being executed