FES underpowered for 18m ship?

As someone who has experience working with EVs, this is alarming to read. Hearing this makes me skeptical of the FES's electrical design as a whole. Your electric car doesn't lose all of its performance if the battery gets to 30% (it does lose some, but not THIS much).

I believe the effect you're describing is the speed of the motor being limited by battery voltage. A well designed system should not have this problem, and this is an indication of a poor battery/motor/propping combo. As Emir said, these motors have a KV parameter, which describes how fast the motor will spin at a given input voltage. As the battery voltage drops, the maximum speed of the motor decreases as well. However, for a well-designed system, this voltage-limited speed, even at min battery voltage, is above the prop's 20kW speed. When the battery is fully charged and the system is capable of producing much more power, the software in the inverter limits it to 20kW for thermal protection.

As Emir also stated, the inverter is most efficient running at 100% duty cycle, but the efficiency hit from running at partial power (switching losses) is on the order of 1-2%, which isn't terribly significant in context of the whole electrical system's ~90% efficiency.

Electric cars have solved this problem, and they have to operate over much wider speed ranges and power ranges. This should not be a problem for props, since they operate over a much narrower speed range.