Although it would be fun to play with, I doubt we would be seeing them in this game. I think the sailcloth has taken the place of the cuckoo as far as a quick item that could help you float slowly towards other locations. Cuckoos do not seem as necessary anymore when Link carries an item that helps him to float in the air that could be used at any time. Much like the Deku Leaf in WW, another game that did not have any cuckoos but had an item that took their place.
However it would still be fun to find them somewhere, maybe just a tiny farm on skyloft where you can pick on them like before. I'm sure for a village like that they have to have some kind of livestock around. And chickens make a little bit more sense than almost anything else given the very limited amount of space they have to live on and resources available. Plus a cuckoo might be capable of remaining on the island while a pig might fall off a little too easily.