Some trolling motors like the Motorguide Wireless do not have a specific on/off switch and they recommend disconnecting while charging. Some chargers do not create the cleanest DC. That, along with the higher voltage to charge, is not always the best for electronics.
When the charger is plugged in, any AC transiets and spikes can get through to the boat electrical system. A switch will usually prevent anything outside of a lightning strike from damage. FF and GPS units just turned off, but power still at the head unit can be more succeptable to those spikes. Most people don't leave those in the boat, more for theft reasons. But, it is something to consider, if you do.
I unplug my trolling motor and FF/GPS when charging.