What makes you think the Yamato II was a failure? The monograph on the subjects seems to present it as having been quite acceptable as a technological development / demonstrator project, which was all it was - the inherent inefficiency of the system was known from the start, and they did gain experience in large-scale superconductor applications.
Maybe that it had failed to be a powered ship that is moving Instead it was ONLY experiment for gaining some new practical experience with MHD technology for different applications. That means that they failed to improve the efficiency.
I think that there is no reason to develop any new MHD ship/submarine without significant step forward in efficiency in salt water. If you want to experiment with superconductors or something simmilar, its much effective and less costly to build some device in laboratory than ship.
The problem seems to be in the configuration of the propulsors. Yamato II used pod-like two units, each with six small MHD thruster pipes. This leads to a massive increase in skin friction and resistance, but was necessary to reduce the gap the M-field had to cover. You'd need somewhat more powerful magnets to be able to use wider tubes or the open "plate" used for tank-testing. The 6-tube arrangement had a nifty side effect - the field lines were constrained into a small cylinder of volume, and so it was safe for an individual fitted with a pacemaker to stand on the upperdeck over the propulsors.