I do not think it crashes. I believe the ship enters the water away from the target, perhaps from hundreds of miles away. It then approaches with stealth then bursts out of the water surprising someone off guard. It's the Titan scene revamped. Of course that begs some questions to be answered...
Should we be considering how it maneuvers underwater? Impulse engines? Wouldn't water touching the impulse engines exhaust generate steam? We can see the shields are down, but perhaps it would be more logical, though not as pretty, if they were up? Do impulse engines thrust penetrate through the screens or is there opening for it to get through? If so, would water get in through the opening? Aren't there supposed to be vents in various areas over the ship? Wouldn't water get into them unless they were louvered? How come it doesn't just float - or sink? Do the warp coils, (hugh magnets
, right?) weigh just enough to make it buoyancy neutral?
Wait, this is Nutrek. Those questions no longer matter, it just has to look cool.