If I were stuck in a Cat 5 hurricane, and I knew that my boat would be smashed to flinders if I attempted to pass the core wall again, I'd look for another way out. One would seem to be to ride in the eye, and I have personally driven in the eye of a hurricane in a car, so I know it is possible to keep pace, but then, Atlantis doesn't quite have its full power left to it. Also, I'd fear the conditions of landfall and then the danger of being left to have the wall pass over me on a potentially exposed beach (which would be the kind I'd be looking for just to beach safely).
That leaves me two options: up or down. Up has problems. The plane overhead can't descend, or it won't be able to achieve liftoff again, and there are no available helicopters. Down also has problems. No submarines, as has been pointed out.
There is another option, but I really don't know the math here. There's another way down. We know that Atlantis is a dive charter. We also know that insurance was set to pay out for all the personal materials seized by the pirates. From the charter way back when with the lesbian and her flirty sisters, we know that Atlantis typically carries at least 4 diving getups. We were given plenty of education about dive belts, decompression sickness, the group's training, and so on much earlier on in the story. Is a scuba tank Chekhov's gun? Will the gang take a dive? Gun, tanks, leftover rope, EPIRB, some glow sticks, and done?
Problems: a quick Google search tells me that one or two tanks would be pretty limited in duration especially given the variance in different atmospheres' depths' compression. How deep would they have to go to survive the stormy seas? Surely not the 200 ft quoted for a sub. How long would they have to stay under to survive the passage of a 20 mph storm roughly the size of Texas? Would Shane be able to regulate his breath successfully after having his heart restarted? Would Trevor pass out from the pain or the blood loss by osmotic effect? Would his blood attract Atlantic species of sharks? Would the beloved chrome plated gun help in such circumstances? How would they all stay together? I dunno, but I'd probably try it myself, as terrified as I am of open water.
If they could survive it, and if Atlantis was destroyed, I'd hope that the guys' novel had been saved on the internet somewhere (verisimilitudinously compared to gayauthors), and I'd feel bad for poor, newly-restored Atlantis, but I'd be happy she made her circumnavigation, at least. And hey, as for that gold carefully concealed in the hull, maybe the experimental sonar developer would be interested in a very late search of the ocean floor, not horrendously farther than he'd originally planned and with the assistance of the Ares/Kookaburra.
Now, what I want to know (and bear in mind I just started reading this all last week, so it's all gone by at lightning speed for me) is what happened with Trevor's birthday, and what did his mother give Shane to hide on the boat?