Intereting point. I believe that a lot of the flux gate magnetometers used for compasses are in the wings - that was in the AAIB report on the problems at LCY from the old rails under the taxiway - so wouldn't be affected that much. I think the inertial navigators use almost exclusively the laser ring gyro, so I doubt they would be affected at all. Smaller aircraft may well have problems, though.
It is historical in origin, like pacemakers in bulk being 'hazardous cargo', because back in the '80s, some were made with plutonium batteries. That hasn't been the case now for over 20 years, but IATA hasn't caught up. Sometimes one wonders if they are still in the age of Lancastrians and Dakotas....