As a side-note, I only knew very few developers who have been using js-ctypes seriously. @noitidart is one, I'm another one, ochameau is another, but I believe that the list is not much longer. We can all confirm that js-ctypes is insanely powerful but also insanely complicated and bug-prone, as well as a major security risk (depending on where you're using it).
I will be somewhat sad to see js-ctypes disappear but I personally believe that NativeMessaging is a much better choice for most use cases. Caveat: I'm not writing add-ons at the moment (rather, I'm contributing to Firefox itself) so I don't necessarily experience the frictions involved.