But there's no air in space either, so aerodynamics is irrelevant. In vacuum, a box shape will travel just as well as a dart shape. The interplanetary or interstellar medium is far too tenuous to generate any kind of drag due to friction (although its interaction with the magnetic fields of the nacelles' Bussard collectors would create drag).
But they would need something a lot more aerodynamic than a big box to fly in a slipstream tunnel! So far the oldest class that we've seen retrofitted with slipstream has been the Intrepid's. Not even the Sovereign-class ships, even with their oblong saucers and sleek engineering sections, have slip-stream capabilities. Obviously the Enterprise-E doesn't have the same aerodynamics as a Voyager (not too mention, but it seems that after Generations
, Starfleet has kind of taken the approach of designing new ships with the ability, either together or seperate, too be operate in planetary atmosphere's and even survive a lot better than the Enterprise-D's saucer in an emergency).