apart from the river activities everything is running as normal in Passau (tours, churchs, shops, cafes, restaurants etc). They are all keenly waiting for you to spend your tourist dollar.
There is very little evidence of the high water except at the very water-front areas. Mostly that is cleaned up and there is some municipal works (pipes, drainages etc) that are no different to the disruption associated with pot-hole repairs.
we were there on Monday 10th. No issues with any town or nearby area tours.