I would honestly vote for vertical nacelles and then to have a back box for a shuttle bay ANYWAY. I don't see any reason why we couldn't have a secondary hull just to have a secondary hull.If only that wouldn't cost the shuttlebay, arg!
As someone mentioned, not having shuttles would be crazy, for a ship that's primarily a survey vessel.
In fact, double that up. Add a secondary hull top and bottom. The nacelles can go at the ends of those. Tons of room for cargo and science labs. Triple wide saucer for all your cargo and shuttle needs.
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