The Nuke boats were much luckier. On the SSBN, we were coming out of PNSY in the teeth of an Atlantic gale. The boat had the usual up and down pitching, and was also rolling very badly due to being round bottomed as mentioned by geetrue.
So it was pitch up, roll to one side, pitch down, roll the other way, for 12 hours or so until we reached deep water. All in all, a VERY queasy ride.
After we reached the dive point, we pulled the plug, and as we got down to around 400 feet or so, the storm surge dampened, and it was a rock-solid ride from then on. Very nice ! So, even if it was "Perfect Storm" weather topside, 400 + feet down, it was movies, ice cream, and soothing music, maybe some coco too.
IIRC there were several accounts of Diesel boats riding out a storm underwater. A lot depended on where they were, too shallow water, like less than 600 feet or so, and the storm surge might ground you. And of course the length of the storm, you only have a limted time under to ride it out. A lot of skippers chose to stay topside, and just ride it out.