Some other places has talked about whether there might have been an issue with removing the original lead ballast pigs and replacing them with a steel keel shoe.
One other issue that has been discussed elsewhere is communications.
Rather surprisingly, I didn't see anything about EPIRBs or PLBs, for example, in the winlink.org article:
On Monday morning, October 29, the tall ship HMS Bounty was in the embrace of Hurricane Sandy 90 miles off Hatteras, NC and taking on water. Doug Faunt, N6TQS, survivor and ship's electrician, told the ARRL that the Bounty crew tried various methods to call for help, including a satellite phone, “... we got nothing when tried calling out on HF. We tried calling the Maritime Mobile Net, but nothing was out there. We had Winlink on the ship that we used for e-mail and accessing the Internet to post to blogs and to Facebook, and we finally found an e-mail address for the Coast Guard. As a last-ditch effort, we used Winlink to e-mail the Coast Guard for help.