Good job! a couple suggestions, though.
1, I'd suggest extruding the "engineering" section from the "primary" hull so that it's all one piece as much as possible.
2, The nacelles have way to many polies. You don't need all of those subdivisions down the length of them.
3, Again, extrude the main body of the nacelle from the bussards to cut down on the number of sections and polies.
Ideally, the model should be all one piece. Lot's of modelers don't concern themselves with that too much though. Still where it's possible without a Boolean it's not to hard to do it.