I don't know of any drop in speed while punching through five-foot, wind-driven waves not uncommon in some of my local waters. In such sees, however, I lower RPMs by 200-300 to reduce speed by about 20 percent to aid in boat control and comfort.
Possibly, not having propellers near the water's surface helps preserve speed when pitching.
In severe enough conditions, I wonder how loading the prop more and less effects overall efficiency, would have to think there is some effect, even if imperceptible to the user.Same amount per hour burn. Just less speed the worse the waves are.
You may do the 200 mile voyage in calm water using less fuel than when rough. But it isn't that you burn more fuel per hour when rough but that it takes more hours to burn (gph) to get somewhere when it's rough.
5 footers on the bays? Really?
What significant differences are you seeing in fuel use at sea versus in smooth water (or calculated), let's say averaged over a long period to account for various sea states?
We monitored our fuel usage from Alaska to Panama, Panama to Trinidad to Florida and on the AICW. The AICW was about 5% lower in fuel usage.