While there are indeed theoretical advantages to an ekranoplan design, there are a number of negatives as well.

Unlike a ship, for example, bad weather pretty much will ground an ekranoplan (I'm going to just use the word "Bob" from now on... that's a long word to type!).

Bobs also have an operational radius of about 500 miles. Take a look at Soviet/Russian ports, and see what 500 miles gets you. Basically the Black Sea becomes the only useful port for a Bob to operate from. Murmansk could also be used; 500 miles covers the Barents, already a Soviet/Russian lake in effect.

While definitely unique in abilities, a Bob's limited operational area hamstring it. There's nothing a Bob can do that can't be done better by aircraft or ships with longer ranges.

Looks cool as heck, though.

I suspect it is because, for military applications at least, the ekranoplans did one or two jobs pretty well, but were limited. So you've got the Lun as an anti-ship missile carrier, and the Orlyonok as a rapid troop carrier.

On the other hand more traditional aircraft and ships could do those same jobs, albiet perhaps less well (so a Tu-22M probably isn't quite as good at flying at sea level compared to the Lun) but could also accomplish other jobs as well. Also they could be easily produced in large numbers by existing infrastructure, where as the ekranoplans were a bit different structurally and of course were a newer concept.