I think you are interpreting the facets of his character a bit too literally. The Eye of Twilight is a metaphorical phrase describing his position as someone who observes both scales of a balance. Twilight is the period of time where night and day (good and bad) exist together. The Eye of Twilight's purpose is, as the title implies, observe the mingling of two very different factors and enforcing the delicate equilibrium they have reached.
Shen is no more ascended than Akali or Kennen are; they have simply recognized the duties of their position, embodying them to the fullest. In other words, they have achieved enlightenment within the parameters of their responsibilities. Shen has undergone a metaphysical transformation, not literal.
Lastly, Shen is not the only member of the Kinkou order remaining. Akali and Kennen are very much alive, not to mention that through his efforts, Shen managed to save many students during Zed's dismantling of the order.