Yes, I understand that an Ekranoplan can, just, fly so can raise itself up enough to clear shipping - at the expense of significantly greater fuel consumption.
But like all these problems, it's the little details that catch you out. You need to know in advance that a ship is there if you are going to gain altitude before you hit it but, even with modern radar, in a big North Atlantic swell, it is very hard to guarantee that you will see absolutely 100% of ships in advance. And those poor buggers who want to sail their yachts across the Atlantic will just have to take their masts down.
But then something like the North Atlantic is just the wrong sort of sea for an Ekranplan. They had no problem flying over a short chop, but quarter-mile-long Atlantic waves (or worse-still two-mile long Mozambique Channel waves) are a real problem as then you have to fly above them with all the fuel consumption that that demands.
I believe Lufthansa used to fly some of their Atlantic routes in ground effect over the Sargasso in the 1930s - even a conventional airliner works as a ground effect vehicle. The arrival of jets, with lower drag at higher altitude, put paid to that.
One more thing that kills these craft is the same as for hovercraft - once they leave the water, regulatory bodies think they are aircraft and they get lumbered with all the associate costs and procedures, which then kills their economics.
