Your boys will have the time of their lives....I promise. We cruised with our son throughout his teenage years and they are his fondest memories. Royal Caribbean has a "code of behavior" that they must adhere to, but unless they are completely out of control, they will not be restricted in any way.
I am not sure what ship you are on, but I don't suspect that smokers will be a big problem. They are restricted as to where they can smoke and it is not too invasive. I am allergic to smoke and have never had a problem on a Royal CAribbean ship.
Hubbard Glacier is GREAT! I think it is more spectacular than Glacier Bay. The catch is that there is Hubbard and another glacier in the area and that is it. However, Hubbard is larger than the glaciers you will see in Glacier Bay. I would not make Hubbard as a deal breaker for the cruise. You will enjoy it.
Have a great cruise.