Bethipooh4--
We just did the 4 night Wonder with a DS 8. He wore long khakis--but then again it was a little chilly those nights. I think you'll be fine. When DS was 6 he did wear dress shorts all but one night on the 4 night wonder (all but Tritons), but now we are moving toward longer pants (DS turns 9 this weekend, in time for the Magic next month). But everyone's child is different, and indeed, it is a cruise to the bahamas, and if khaki shorts is your pick it is fine. And I think Disney's own guidance with respect to children under 12 or so is that Mom & Dad know best.
Have a great time.