Re: "whether the Navy should be abandoning low-tech backup solutions"
All this brings to mind something I was told (and could be an urban legend).
At one point the navy insisted that the on-deck electronic fire control system for some weapon or other be able to withstand the heat flash of a nearby nuclear detonation. The manufacturer questioned that requirement as the heat flash would kill the operator. The reply was that they could always send up another seaman from below decks.
So EMP hardening isn't necessary as long as they have sufficient spare iMorseControllers below decks.