I know that you burn more fuel in rough seas due to the loading and unloading of the motor rpms. I would think that it is not detrimental but smooth water is a lot easier on them. Maybe it's just me due to age, I'm not fond of the rough stuff, but do catch a lot more fish when it's rough than calm. Just my views!:letsdrink
Not trying to be cute, but I don't think the motor knows a rough sea from a calm. The prop has enough slipage that the engine is not going to be over torqued. The occasional wave breaking over the motor might be a concern.
I think it's all in how you drive it and how hard you push it.
Well, also note that in a rough sea, and your pushing pretty hard, you can see the motor shaking quite a bit more. I dont think the internals of the motor care, but I'm sure it could put more stress on the transom of the boat and motor mounts. But I'm sure they designed the mounts to handle plenty of excess force...rotten transoms are another thing!
instead of posting this couldnt you have really thought about it? not trying to be an ass but, is it hard on a trucks motor when you take it off-road and threw the mud for a period of time? of course........ the motor is gonna take a bit more stress doing things like that, rather than cruise on flat or low level water.... kindda like a truck being on a paved road..:doh