Well, it was "unexpected." And don't get me wrong, the ship rising out of the water is, in and of itself, a cool shot.
What makes it bad writing to me is that there is no explicable reason for it to happen except to get the cool shot. Kirk is, we are told repeatedly, a starship Captain of greatness. It could not or at least should not have failed to occur to someone fitting that description that just keeping the ship in orbit would hide it from the natives and allow it to better support Spock's operation in the volcano*. That's why the ship on the sea floor is "unexpected." There is no good reason for him to do it.
The plot requires Kirk, in other words, to act stupidly in a way that has to be lampshaded by his Chief Engineer -- so that the viewers will know not to take any of this seriously, because the writers sure didn't -- in order to get a cool shot. That it was good spectacle does not make it good writing. Having to contrive stupidity on the part of supposedly-capable characters is bad writing. Good writing would have been to find a means to the spectacle or something like it without having to resort to that kind of contrivance.
I'll have to respectfully disagree with you.
The fact that it's unexpected has nothing to do with Kirk's reasons or lack of reasons for putting the Enterprise under the water. It's simply because of the juxtopositon and contrast of a giant space ship in an environment that we haven't seen it in before.
The film only barely gets into the technicalities of the situation our heroes are in, and for me that's the way it should be. We have almost no information on why the Enterprise is hiding down there and we don't need it. Mostly because a good portion of the audience doesn't care. I get that you do, and that's cool, but pretending that it's some objective yardstick by which to measure the quality of the writing in the scene is intellectually dishonest.
(* Which, even worse for scientific illiteracy: "cold fusion" does not freeze things. And I actually have to wonder if the writers just didn't know that, or knew and just didn't care to come up with an alternate name for the device, like a "stasis bomb" or something. It's a moment of gratuitous badness that a simple copy-edit should at any rate have caught, which really does create the impression that nobody of importance on the production cared at all. I'm not one of these people who believe the filmmakers should be "respecting the fans" at every turn -- but not respecting your own craft and product is a different kettle of fish... and one of the reasons I hold it against Abrams is that I know for a fact he is, or can be, a better filmmaker than that.)
Even setting aside that things like warp drive and the transporter are laughably unscientific, you're making a huge leap here.
The writers obviously not caring about the specific made-up futuristic technobabble reasons for a Starship being underwater or how to stop a giant volcano.
The writers obviously don't care about anything.
The truth is that you seem to care about these kinds of things in the fiction you enjoy, and the people who made these films seem to not. The only thing that proves is that these movies are not to your taste.