1. The passage is not trying to make predictions about how ocean water moves, it's trying to say something about how lost atheists (?) are. It's doing that by emphasising that they are not just 'in darkness' but are wrapped in layers of ignorance.
Think about it a bit. If the ocean is calm you can see down a long way but, if it's choppy then the crazy refractions make it hard to see down at all. Similarly, clouds make it hard to see very high and darkness makes it hard to see at all. The Qur’an is saying that many things are involved in an athiest's non-belief. The practical upshot being that you should expect to convert an athiest with one simple truth.
(That's IF "athiest" is really getting translated correctly. Are you sure that's right?)
2. The article you quoted is talking about a very special kind of wave, not ANY kind of wave. Heck, any kind of sound underwater would count as a wave!
P.S. Interesting - note that Allah is granting the light to individual people. It's not the people giving it to each other or discovering it for themselves.