It was never addressed in canon.
The episode to which you refer, "Force of Nature", occurred in the last season of The Next Generation at a time when most of the effort in storylines was geared towards Star Trek: Voyager and Deep Space Nine: the developers of those shows didn't particularly focus too much on the continuity issues introduced as The Next Generation was wrapping up. Indeed, even The Next Generation writers ignored or found ways around it for the remainder of the season.
However, according to Memory Alpha:
According to the unpublished VOY Season 1 edition of the Star Trek: Voyager Technical Guide, by Rick Sternbach and Michael Okuda, it was suggested that because of the variable geometry pylons, warp fields may no longer have a negative impact on habitable worlds as established in this episode.
But since the manual was never published, it's not canon. Alternative theories include:
- In Deep Space Nine, the Dominion War was more important than an environmental concern.
- In Star Trek: Voyager, they were so far away from the Federation and getting home was such a huge priority, any non-core regulation artificially limiting their ability to travel was summarily dismissed.
It's also interesting to note that the issues raised in "Force of Nature" are referenced, indirectly, in the last season Voyager episode, "Renaissance Man", when the Hierarchy attempt to trick the Voyager crew into ejecting their warp core because they entered an area that's occupied by people who believe warp drives disrupt subspace.