For that age, I don't think anyone would object to nice shorts. For "little" boys, I'm in favor of making sure they're comfortable. The zip offs sound like a nice idea though since the dining rooms can be chilly.
Definitely DON'T buy long pants just for the cruise, especially on the Wonder which doesn't have a formal or semi-formal night. Since I believe the adults are now permitted to wear nice jeans, I think that would be fine for the little ones also.