I think zesuaium still has a place in the setting, but it's likely for very specialized equipment. For example, it would seem like several tools using aether would be unfeasible without zesuaium components.
As for its scarcity, it could just be hard to manufacture. Harder than Yamatai can easily manage now. You might simply not have the luxury to armor something wholly in zesuaium if you need zesuaium in the build-up of more important components such as ship propulsion systems.
To me, the above two paragraphs would strongly motivate why the era of million-ship-strong fleets and wholly zesuaium-coated armor is drawing to an end; and why we're seeing Durandium, Yama-Dura and Yamataiaum coming to be more prevalent.
It think this is okay. Zesuaium should stay in the setting. In fact, I think the material's usefulness and specific applications actually characterizes it much better. Before, it wasn't because it wasn't rare and you'd see it used practically everywhere. Now, it's pretty much an important staple of yamataian technology which is judiciously applied rather than overused.
This is a good thing.