Jet planes can drive along a highway, but they make for poor tow trucks. And there would be all sorts of interfacing issues that get complicated when the space between the two sides is filled with water rather than with nothing. Dedicated underwater rescue gear might indeed be vital and in existence. But probably not of great relevance in a fast-paced action sequence involving a villain making his escape to space. Or whatever.
How deep can transporters penetrate into ordinary seawater? Two klicks of basic if cave-ridden bedrock is already a problem ("Bloodlines"), and water might be worse - but San Francisco Bay isn't all that deep. We just don't have much data. Scotty's whale-saving operation involved depths of a dozen meters only...
The dikornium cloud creature entered the ship through the radioactive disposal vent for impulse engine number 2.
And then proceeded through the ventilation system to Garrovick's cabin. So, the cabin was directly open to space all the time?
Apparently, the cloud creature getting in involved going through some structure or material that didn't let air out. And I doubt it was a classic mechanical two-door airlock, as the creature never demonstrated an ability to operate machinery. But a random gas cloud probably wouldn't get in; it would need intellect, the ability to exert force, and possibly also some of the dikironium critter's special tricks for that.
That crash looks like a relatively low-speed one. A ship falling all the way from space would probably create a drastically different-looking impact mark in reality, but we can forgive Hollywood for that. Yet a ship falling from space would be unlikely to hit San Francisco Bay rather than some other random area of the Pacific or of dry Californian land. Do starships in nuTrek regularly operate from the surface of Earth, perhaps? Or does the protecting of SF Headquarters from anticipated threat routinely involve lowering a starship or three to rooftop level?