The aerodynamic benefit of flying in ground effect is fairly small, and the disadvantage is that rogue waves can just randomly splash that high. The current plane's wingspan is 65 feet, which probably means it flies about 32 feet (half a wingspan) off the water. Rogue waves can easily be that high in mild weather, and hitting even a small amount of water at 200 mph (claimed cruise speed) is bad. Lots of sea birds too…
This feels like something that an automated system could pretty easily detect, up to the range of visibility, and raise the seaplane up if this happens.
Further, this is an inter-island route. Adding dedicated monitoring seems imminently doable.
Yes, this is a concern. No, it's not hard to deal with.