If you look at a navagational map of Southeastern Alaska you will see that much of the time there is land on both sides. There really is no good side or bad side. And when near the glaciers they very slowly rotate the ship so that everyone gets a good view.
Doors and ceilings can creak in any catagory of cabin; I have had this happen a couple of times; but a call to Passenger Services and it was fixed the next day--usually a couple of well placed shims do the job. And the only time I've had a balcony door whistle is when it was not closed all the way and latched. And if you leave it open the wind can whistle through the entry door. If it's annoying just shut the balcony door.
kmathi, I must agree with Nadine and janfred: if ever there is a time to get a balcony, it is on an Alaskan cruise . . . .well, that and a Panama Canal cruise too.