Good question. The ship design of the MOO series is linked to the ship combat game mechanic. The latter, being tactical combat, can be poorly represented in a Civ environment, which focuses more on strategy. So far ship design is represented by the promotion system: as the game progresses, you get access to more and more promotions. (As I mentioned earlier, these mostly give a 10 % increase in strength - or defense -, a result of the abandonment of the ADM values of Civ1-3 in favour of a single strength value.) In short: we're in a different environment here and MOO specifics can only be approximated. Hence MOO2Civ.
BTW, in answer to an earlier suggestion, I see no reason why there shouldn't be room for a MOO3Civ - provided there's enough support from creative MOO/Civfans, ofcourse.