As I recall, the "Writer's Technical Manual" that Rick and Mike wrote for the writers on Voyager also notes that the nacelle movement also helps protect subspace from the deleterious effects of warp travel.
Myself, I just went with the idea that it was part of a variable-geometry warp bubble designed to optimize the bubble to the warp factor based on one of the concepts at the end of the TNG Tech Manual noted Star Fleet was considering such a thing (the concept vessel with the nacelles that traveled back and forth across a set of "wings").
Myself, I just went with the idea that it was part of a variable-geometry warp bubble designed to optimize the bubble to the warp factor based on one of the concepts at the end of the TNG Tech Manual noted Star Fleet was considering such a thing (the concept vessel with the nacelles that traveled back and forth across a set of "wings").