In this question, the Intrepid Class' folding nacelles are explained as a feature designed to circumvent the problems stated in TNG 'Force of Nature'. The Sovereign Class and Intrepid Class came into service around the same time. The Intrepid class has these new folding nacelles, the Sovereign class seems not to (at least there is no mention of this on Memory Alpha and I for one don't recall seeing the Sovereign class folding its nacelles). In-universe then, why didn't the Sovereign class get folding nacelles?
More on the folding warp nacelles:
According to the unpublished VOY Season 1 edition of the Star Trek: Voyager Technical Manual by Rick Sternbach and Michael Okuda, (p. 12) it was suggested that because of this new folding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.