My premise: the SS Emmette has no windows. So it is a prototype to test higher warp speed. Therefore there will be no "luxury rooms" and a normal ceiling height of 2,5 m. The rest of the ship is full of technology.
The ship is 131m long. If the ship (like the model kit from Fantastic Plastic) would really be 95m long, then the deck would only have a high of 1,8 m.