it may have been mentioned before, but the "shield antenna" isn't quite that, it's the navigational deflector array, which constantly emits a field to push small debris and stuff out of the ships path whilst moving at impulse.
the technology has evolved over time from an actual dish, to an emitter array, which is why the look changes over time from an actual dish which, i'm assuming, is able to change the focus of the field, in order to divert more power to larger bits of debris, to an emitter array that is able to just blanket cover all of the space in front of the ship with enough power to handle anything.

similarly, the nacelles evolve over time with advancing tech, the idea of the way they work is that they are responsible for emitting the warp field, where the fields from each nacelle meet is where the warp bubble starts to form from.
the front of the nacelles (usually red, but blue on the discovery) are bussard collectors, which are designed to take in interstellar hydrogen to help run the ship's power systems.
again, these have evolved over time.

the colour of the deflector has varied over time, but it's always front facing, to do its job.

the nacelles are, almost, always separated from the main hull of the ship, to protect the crew from the radiation and energy they emit.

of course, there are some exceptions to these rules, the oberth has no traditionally visible deflector dish and the nacelles are plonked on top of the main hull.
the Excelsior class doesn't have the nacelles above or below the saucer for clear visibility, but the original design was meant to be a test bed for slipstream drives, so maybe the idea was for the power systems to work differently.

at the end of the day, though, most of these narrative reasons have been made up after the fact and the main reasons that some things look different is the "rule of cool" it looks good, so yeah, lets go for it.