Meh, not that many natural disasters. We’re not at risk for earthquakes, tornadoes, volcanoes, it’s only large winter storms and hurricanes. Given that this wouldn’t be anywhere near Williamsburg, which is in Brooklyn, but in Manhattan and likely to have a door to keep rain out in the first place, it’s less of a concern.
It’s not the 1 line down at South Ferry, it’s not the PATH train, right next to the Hudson, it’s like any other basement in town and not as prone to flooding as you suggest.