The planet they're on is experiencing seismic and volcanic problems, probably threatening the local sentient life, hence the duckblind.
The Enterprise may be conbining hiding with taking point blank readings much closer to the magma pockets and tectonic plates at the ocean bed.
With the new transwarp beaming technique they can even beam to and from the ship through the planetary/oceanic mass.
It would be an extreme solution to those problems, though. To that end, doing it for character reasons within the story could be more important. I'd like to think, who else but Kirk would take Starfleet's flagship underwater?
In other words, even if there is minimal danger to the ship, it's still probably considered a wreckless act that is generally frowned upon among the admiralty. The mission we walk into in the first nine minutes could be what leads to Pike's lecture Kirk. A lecture which may include the question, "Did you really submerge the Enterprise?"