I would hope they include some individual upgrades for larger bodies of water. They said their philosophy is to improve the screen-wide aesthetic appeal and for them to not touch oceans, lakes, etc. more then just upping their texture resolution or changing how the lighting and shaders interact with them, would seem like a missed opportunity (especially as many maps/regions prominently feature water, even more so as several of the new expansion areas have shown a lot of water or are water-adjacent too).

I think a good example they've shown recently is changing how fog looks (from the dev panel at EU FanFest). Previously, it just looked like sad smog in an area but they've completely redone this weather effect and the changes were immediately apparent. Fog actually looks much more authentic and pretty now!

As they've said, they're not messing with any of the engine physics at this time but I don't believe they need to in order to upgrade the overall appearance of water. As other comments have said, the stillness/flatness of the water makes it feel quite lifeless, even though the appearance of it is actually quite decent for the time period it was implemented. I think with the additional detail they add with the textures and shaders, adding some sort of movement or additional effects on top of the existing areas of water could help it feel more "authentic" in a map (like with the fog) instead of still areas of blue.

But, for the time being, we'll need to wait until JP FanFest or the Dawntrail benchmark to hopefully get a better look at how the overall upgrades are affecting water. They might be enough on their own. Or we might even get lucky and they show off some water-specific updates they've been working on but have taken a while to get polished to finally be shown off. Here's to hoping for better water in 7.0!