I'll wager that it's extremely likely that we'll one day have a ship that looks like the Enterprise. Not because it's practical or efficient but simply because once space travel be cheap and artificial gravity be perfected, we can make a ship look like anything we want -- and I'm pretty certain the Enterprise has become embedded in our pop culture such that someone will want to reproduce it.
There will also be ships shaped like Star Destroyers and maybe the Discovery.
As for whether or not ship design would have evolved to include an Enterprise shaped ship in a world where Trek did not exist, it all depends on the contributing factors. Assuming a ship need two big engines, and that distance from the ship be desirable, then having them on nacelles makes sense. Designs that incorporate circles are more volume efficient so cylinders and saucers are appropriate (though spheres can be better). Symmetry is always nice where thrust vectors are involved, but with artificial gravity and energy shielding, one doesn't needs an armored chunk as the base hull -- delicate bits are fine.
In other words, the Enterprise is a plausible design. And for the time, a rather revolutionary one. Up to then, the V-2 was still inspiring TV ship designs. It was rockets and flying saucers (Lost in Space; My Favorite Martian; Forbidden Planet).
An inevitable one? Not pre-1966, but almost assuredly post-1969!
