What about rogue waves? Ekranoplans would have to be able to detect and fly over rogue waves and ocean storm swells. Rogue waves don't occur that often, but ocean storm swells do. As you point out, it routine now to detect storm swell conditions.
> It can carry enough armor to make it immune to anti-air missiles, yet it is fast enough to escape anti-ship missiles.
I don't think it would be hard to redesign anti-ship missiles or AA missiles used in look-down/shoot-down systems to negate any evasion advantage ekranoplans would have.