Which animals live in trees and make noises like rubber ducks at night?
It is most likely a Tawny Owl (Strix aluco), or Waldkauz in German, one of the most common owl species in Central Europe. These owls have many different calls, and you can hear them often here in Karlsruhe at night. Particularly their "kewick" call sounds similar to squeezing a rubber duck. It is usally emitted by female individuals during the mating season, but also males can produce it. Juveniles have a similar call as well. But most of the time - as far as I have noticed - you only hear their more common "hoo-hoo" calls (listen here or here).

Photo of a Tawny Owl:



Image Source: 

https://commons.wikimedia.org/wiki/File:Waldkauz-Strix_aluco.jpg