Yes, the advanced "plug in" cloaking device witnessed in the "The Enterprise Incident" suggests otherwise, but if these are not portholes on top of the BoP, then what are they?
On the contrary, I'd dare to say that your theory is upheld by canon, especially "The Immunity Syndrome" where warp and impulse power were combined to achieve one major forward thrust.
The one thing I cannot get out of my head is the recurring theme of sailing ships in the context of Star Trek. Essentially, the Enterprise
has more in common with a submarine in space, so what in space could possibly qualify as an analogy to wind to propel a starship?
In "By Any Other Name" Spock said that the Enterprise is propelled by matter-antimatter reactors (or the energy these provide).
Both matter-antimatter annihilation and nuclear fusion yield gamma radiation which is also abundant in space. Could it be that gamma radiation is the "wind" that energizes the warp engines and to have higher performances you just add extra radiation?