are you sure you it's a large hull ship, not a huge hull? 9 logistics should be the default cost of a huge hull (or maybe that's already including the -1 logistics cost). a large hull costs 7 by default, 6 with the HLS.
the adjacency level has nothing to do with ship logistics cost. it's just an increase of the total logitics value (fleet size) - basically the same type of bonus you get from the various logistics techs.
