The steel box (ship) may provide pretty good EMP protection depending on lots of unknowns. We pretty much know what will happen if an EMP hits the electric grid because those long transmission lines make excellent antennas and feed lines to transformers and customers.

But a steel box sitting in muddy water may do just fine. Radios on the bridge may pop, expecially any with long whip antennas, but equipment inside the hull may survive ... or not. Do not assume gear will be safe or will burn out. Propulsion and steerage may function fine despite the electronic navigation and comm systems dying. Regardless of all the theories, there is little empirical evidence either way. IMO

Here's a thought. Put a Marine VHF handheld and a GPS rcvr in an ammo can as low in the ship as possible, isolated from the hull. Essentially a small faraday cage.