We have just been on the Alaskan Cruise with Celebrity Cruises and no it doesn't really matter which side of the ship you are on when visiting the Hubbard Glacier the ship does a complete turn round in the passage so that you see all sides of the hubbard.
The answer is the obvious one - if you're sailing North you will see more land on the starboard side, if you're sailing South you'll see more land on the port side. There's usually a couple of days cruising - some of it through the inside passage where you might see land or ocean either side. When sailing in to see glaciers the captain usually turns the ship round when you're up close.
We had a grat time and the best trip was a helicopter to land on a glacier - a real one-off
Just a small addition.... Many ships have cabin over the stern of the ship, these are often the first to go because they are sought after but they give a wonderful view, the balconies are invariably larger and you are shielded from the wind. Lucy Bonnette.