Oceans: We know the basic mechanics of currents, tides, chemistry, where all that water came from in the first place, and while there are a few known-unknowns it doesn't seem like a paradigm-shifting discovery is likely. They mystery is mostly because it's huge and we just can't look through it very well, and that there's too many physical inputs to track them all so models are abstractions by necessity.

The same goes for most of your list (I will not speak to prime numbers, I am an Earth Sciences guy and bad at higher math) in that we may not have a perfect map but we know the shape of it and where the probable gaps in understanding are. So the "why" is questions like "why do waves happen" or "why does the sun look yellow" or "why do we have embryonic 'gills'" and we have pretty good answers you can drill pretty deep into.

Pushing at the edges of physics is, I think, where the situation is flipped. We have very good models for the behavior of light but questions like "why is there a limit to the speed of information and why does light go that fast" and "why does it behave as a wave and also a mass-less particle" don't seem to have satisfying answers or even a means to be answered. Admittedly physics beyond its applications to organic chemistry is outside my education (again, math) but I try to keep up.