Depends on viewer height. There are 3 scenarios.
If your viewer height is above wave height then the wave will block less of the distant object than its own height because you are looking down and over it:
If your eye is at wave height then the wave blocks as much of the distant object as its own height as you are looking straight across the top of it:
If your eye is below wave height then yes, the wave will then block more of the distant object than the wave's own height:
And the closer the wave in this scenario, the more of the building it will block:
So, if your viewer height is low enough then waves would be an explanation for you not being able to see distant objects.
If you're at any reasonable altitude then unless there are massive waves - which there typically are not - then waves cannot be the explanation as you are above wave height and thus the waves cannot block the distant object. A dime CAN block your view of a distant elephant but only if you hold the dime close to your eye. Put the dime on the ground and you'd have to lie on the ground and close your other eye to get low enough that it can block anything.