I have now for a long time been searching for living ducks in any part of eso, but only found the dead ones in hunter huts. So, a theory came around and wanted to see if it made sense.
Sheogorath has taken all the living ducks into one of his realms. Or alternatively he has turned all ducks into other critters. Since he will be changing into his true form in the relatively near future (in game at least) it will explain why they can also be found in later era's.
Does this sound in order?
The duck awareness guy.