I think what was meant were the direction of travel of the wave as one axis and the height as the second axis. The third axis would then be the direction along the length of the wavefront, as seen from above.
The assumption was that this third axis was irrelevant with respect to the wave's breaking behavior and max height - so simulating waves in a narrow channel of water would be the same as simulating waves in an ocean (as far as max height is concerned).
This paper now showed the assumption is wrong, and interactions parallel to the wave front (or coming from yet other directions) also influence the max height.
My SO is in the physics field and I can tell you what is almost certainly the sad real reason. It was easier to publish/finish the work with only two dimensions. The results were "good enough" , after that it became standard and people just built on or referenced that work. So they too could publish a paper.
There was an article on top of HN for a while this week talking about academic fraud and such that has more unfortunate info on the cutthroat nature of research.
Physicists are famous for simplifying reality. See 'spherical cow in a vacuum'. This isn't fraud or laziness. it is just that reality is complicated and messy and these sort of simplification are often necessary for making any sort of progress on a problem.
I mean, there is nothing wrong with simplifying your assumptions - spherical cows etc - if it let's you avoid a whole lot of additional complexity and still gives a useful model - and I think that was the case for the "2D waves" assumption. So I wouldn't immediately call it fraud.
The danger occurs if people take the model as orthodoxy and dismiss any deviation as impossible.
I think in the case of "freak waves" you could actually watch the change in public attitude over the last decades: They used to be seen as physically impossible and basically sailor's yarn - until eyewitness accounts kept accumulating. Eventually, we got empirical evidence in the form of satellite images and they were accepted as a real, if unexplained phenomenon. And now we seem to be getting the first verifiable theories that offer causal explanations and allow to predict and reason about them.
All in all, this seems like a good example of scientific progress to me (except it would be nice of we could get to this point earlier in the future with fewer lifes lost).
This is one of those "truisms" people use to justify bad behavior rather than the authors intent. Using 2 fields to represent a 3 field system because it is easier than a more complete model, is exactly the type of thing this saying is warning about.
Has it really? That seems unlikely to me. I am not even sure what the two dimensions would be, looking at the water from above or from the side?