The warp nacelles had the ability to be raised into position for warp speeds, then lowered into a more streamlined position when at slower-than-light speeds. The Intrepid-class starships were equipped with this feature, examples of which include the USS Voyager and the USS Bellerophon. (VOY: "Caretaker", DS9: "Inter Arma Enim Silent Leges" et al)
The Intrepid-class was the only known Federation starship class to incorporate this design feature. The first time the concept of variable-geometry warp nacelle pylons was mentioned anywhere is in the Star Trek: The Next Generation Technical Manual (p. 178) in the section dealing with preliminary concepts for future starships. The goal of these pylons was to improve engine efficiency by optimizing field stress when the ship travels extended journeys at warp 8+ velocity, resulting in significantly improved engine efficiencies.
Actually, while not specifically mentioned in writing, the concept was already explored in 1983 on one of Bill George's study models, based on a design by Nilo Rodis-Jamero, for what was to become the Excelsior-class, slated to premiere in Star Trek III: The Search for Spock. At the time however, the variable warp nacelle variant was passed over for a fixed pylon variant. Yet George's study model did make a canon appearance in the debris-field of Surplus Depot Z15 in the Star Trek: The Next Generation episode "Unification II" with its nacelle pylons in a raised position.
According to the unpublished VOY Season 1 edition of the Star Trek: Voyager Technical Manual by Rick Sternbach and Michael Okuda, (p. 12) it was suggested that because of this new folding wing-and-nacelle configuration, warp fields might no longer have a negative impact on habitable worlds as established in TNG: "Force of Nature". According to Star Trek Encyclopedia (3rd ed., p. 555) these nacelles did in fact prevent damage to subspace. According to comments by Michael and Denise Okuda, when mentioning of the speed limit was abandoned a few years after "Force of Nature", it was assumed that newer ships, such as the USS Voyager and USS Defiant, had improved environmentally friendly warp drive systems, that did not cause damage to the spatial continuum.
VOY Season 7 episode VOY: "Renaissance Man" however suggested that the warp drive of the Voyager still caused the cumulative damage. In the episode, members of the Hierarchy capture Captain Janeway and demand the warp core of the Voyager in exchange for her. The Doctor comes up with a lie for the crew of the Voyager, that they had entered R'Kaal space, a species of ecological extremists he had invented, who had supposedly outlawed warp travel in their space, because conventional warp engines damage subspace. When he claims this is the reason why Voyager has to surrender its warp core, the crew makes no effort to convince the R'Kaal that their warp drive is totally environmentally safe.