And the greatest change JJ Abrams has ever made to the Star Trek universe: He brought the prime directive back to sanity. It's okay to save aliens' lives so long as they don't see you! Screw you Phlox!
So what if a handful of Nibiruans saw a colossal... thing... rising out of the ocean? Most ancient cultures had stranger tales than that in their mythologies.
What was the point of the underwater ship anyway? It's a hiding place? What a ridiculous way to hide the ship. Considering the state of technological development on Nibiru, the Enterprise crew could have operated freely and without risk of being seen simply by working at night.