That's what I mean, it's one thing using nuclear explosions as a means of propulsion, but using it to slow down from like 1/3 light speed or whatever the fuck you'd need to get to Tau Ceti in 200 years... that ship is going to take a hell of a beating, shit, even the Vengeful Spirit is probably going to be feeling it taking nukes to the nose for hours at a time...
The scene on the Battlestar Galactica remake, where Galactica tanks a Cylon nuke, I've got a book written by the guys that were the tech advisors for the show, and real physicists, and they were saying despite the less effective nature of nukes in a vacuum, it's still got to be tough to tank a nuke going off right next to the hull, and they worked out the hull plating on Galactica would have to be 5 meters of Tungston Carbide to take a 100KT nuke like that, if it was in contact with the hull when it detonated.
And that was just one.
The Ark's going to be flying into hundreds of them, one after the other, and not using it to be pushed away by ablative plate vaporizing, but to slow down from 300KPS or whatever crazy speed Pat said.
The Spirit could probably take it, but anything less tanky than that...I'm pretty sure the guys that came up with this propulsion method abandoned it for a good reason.