I suppose wave motion may have been a factor, yes. Certainly it seemed to me that waves were hitting the front of the hovercraft and spraying all over the windows. I just think that the propeller vibrations were probably much more significant.
Someone upthread suggested that hovercraft need reasonably calm seas - I don’t know about this, but will probably be safe in assuming that that poster knows more than I do about the subject.
From what I remember, it’s a different type of movement. I went on the cross-Channel hovercraft a couple of times, and you didn’t get the rolling motion that I imagine would provoke sea-sickness (I am lucky in that I have never suffered). Instead it’s more like a series of irregular and sudden bumps as the craft bounces off the waves. Not particularly comfortable, but seasickness sufferers would probably find it less uncomfortable then the pitching and rolling of a traditional ferry. Plus, of course, the actual crossing only lasted about half an hour instead of 70-80 minutes or so for a normal ferry.
Not sure if they are still in use in Hong Kong for the commute to Discovery Bay. They were pretty fast but noisy and bumpy as well. I think they were supplanted by much bigger ferries. The Disco Bay hovercraft were pretty small and seated maybe 50 people.