Indeed.
I read such things as well. Jack London wrote a story (in the 20's? Set in the 20's? I could be way off) about such a situation, and my copy of "Earth Abides", which I was required to read in high school several centuries ago, I still have.
I'd think that the Naval Observatory (designed for 'Naval' gazing? LOL!) would be a poor choice for such a shelter. With so much of the Earth's surface covered with oceans, it'd likely be inundated. Even if the shelter had the characteristics of a submarine, there'd still probably be tons and tons of debris on top of it when the water receded. Way too close to the water.
Agree with your point about us knowing by now.
Sandia Labs Comet Strike page
http://www.sandia.gov/media/comethit.htm
Article about LANL research on strike induced Tsunamis
http://www.xs4all.nl/~carlkop/strike.html