We haven’t found this to be an issue when using a lithium battery, because it essentially just re-charges it. The resulting voltage spike is small enough and for a short enough duration that it hasn’t seemed to have a measurable effect on the other electronics that run directly off the battery voltage, particularly given the significant braking effect of the water itself once the thruster stops being commanded to turn.
There have been some limited reports of issues when using some non-battery (surface-based) power supplies, which there are some tactics for dealing with discussed in this post 