As far as movement penalties I have never noticed that mainly because they were rare events away from a hot spot. So I never had much traffic in a flood zone.

As far as I know there are no economic penalties minus the damaged buildings wich you can repair along with the reduced population wich in turn makes the city less profitable. If you look at the settlement details and theres a lot of devastation, then it may have been from a flood, but again it could be annoying rebels.