Was George Orwell an Optimist?
Abdullah Ibrahim - Water from an Ancient Well
So I guess this question was never officially answered (and there's two conflicting responses in this thread)?
I think this post by the designer supports Brian's answer, that the three ship per type limit is imposed per player, not per color controlled.
The Rebels and Imperials get only the listed number of armies total (not per army color). The second set of armies is only used during play if there aren't enough pieces left in the first color to place reinforcements.
The extra color provides you with more figures if you need them, but doesn't imply that you now have two independent forces which would each have their own ships.
 fixed the link.