I can so see the evolutionary lines here... Initially, most of Earth's combat warpships would be of a type that takes off from planets, hence the lifting body shape. They'd perhaps need to roost on a surface installation since there wouldn't be suitable spaceborne facilities yet for servicing these complex things - but they'd be more ruggerized than their civilian equivalents, and more generalized as well. Landing on a faraway planet, be it own or enemy, would be on the agenda, even if that planet didn't have a proper starport.
The Emmette would have a relatively primitive sublight propulsion system, and perhaps wouldn't be completely armored but would only have an armored bow section (as outlined on the model). The Iceland would have the proper impulse engines and the complete polarizable armor cover. It would only be after this that Starfleet would move towards completely spaceborne starships - echoing how combat submarines went from briefly diving submersibles to completely underwater-fighting vessels during WWII.
Perhaps the Emmette and the Iceland would be largely incapable of interstellar operations, using their warp engines for rapid insystem transit instead, and doing a lot of stuff in planetary atmospheres. Only in desperate situations, such as "Twilight", would these relatively slow vessels try to reach another star system.
Young Nat Archer's model ship might not be a combat vessel yet, given the NASA style paint job. The shape (and the black-white surface finish suggestive of heat shielding) would reflect the need to do maintenance back on Earth's surface, though, or perhaps suggest a mission of landing on other atmospheric worlds such as Mars or Venus or Titan.
None of these lifting-body ships have bays for auxiliary craft in evidence, and could be argued not to need any. All sorts of sliding panels on the hull could still be postulated, hiding weapons and sensors and docking ports. The need for such smooth paneling would be decreased on the Intrepid, Enterprise and Columbia because those wouldn't spend much time in atmospheres, so the weapons on those would also be more in evidence. But we could blame residual "must-cover-everything" thinking from Iceland on the sparsity of visible weapons on the Intrepid (which only has the two bow torpedo tubes and none of the naked gunports of the Enterprise).
Timo Saloniemi