I was on Pirates on Monday January 7th and there was a prolonged breakdown. I don't know about any sinking, but this is what I do know.
The boat I was in ground to a halt by the Davy Jones/Blackbeard projection. Looking back at my phone, I sent a text to my wife (yeah, you can get a signal on the ride, I was surprised) saying "I'm stuck on Pirates of the Caribbean" at 1:54pm. At 1:58pmI sent a text saying that they'd turned the sound off. At some point they turned the mist off and the lights on. The projector kept projecting, I could see Ian McShane's eyes being beamed onto the empty seat next me. The next text I sent said I was walked off the ride (I was right next to a walkway) at 2:19pm.
I took a little bit of video of the tunnel while it was lit-up.
Stuck On Pirates January 7th 2013 - YouTube
You can see a cast member standing by the green door where I was walked out. It lead to a flight of steps, into a corridor full of baking bread, another flight of steps and I came out of some swing doors next to the restrooms near the Railway Station.
So, I don't know about any sinking, but there was a long delay on the ride last Monday.