Interesting points!
If I can add, there ARE actually people with whom you can talk about the Black sea and Waterway landmarks. Maybe more people could have extended topics on some locations but as it goes, there are people from camp Hathor and Junkyard that reference Rig and DnD, also ferry(wo)mans can also talk about Black sea and their limited experiences with it.
I guess it makes more sense for people to have some wild guesses because that location is wrapped in mystery and death by pirates and poisonuos creatures.
As for the actual locations in water, there are some hidden ones as well as some quest/event related ones, waterways are busy place during Pirate questchain also!
If there were more time devs could add Upper cave waterway ring and some related places/events for example. As things go I am more in line only if there was something meaningful there...
I actually don't know if Ray open up his shop before you can start the expedition content but if he does (after visiting the place for the first time) that's cool and it is already a solution in a way.
If that's not a case then I suppose that getting Jetski earlier could bring some problems and one of them could be getting to the Black sea before Aegis which promptly locks you out of it and that could be a pretty big confusion for a first time player just for a "casual" exploring.
I would not mind though if something could be added for a limited exploring, some quest and a Junk-junk Jet (Shoddy shotgun of the JunkJets) which moves horrendously slow and can't overcome even some weaker currents.
It could also add some incentive for (nevermind that people would laugh for your junk) resolving some quests like Gorsky warehouse earlier with jets without waiting after expedition or after stealing Rays JunkJets (is that still possible? With JunkJets outside? I didn't play burglar character for some time, would like to try that one)
In any case, it's on devs if they can or would like to further improve on it.
I really like your idea of subtle and casual references to waterways and maybe we could have more of these!