The Dominion may have wiped out the active Maquis body, but did that still solve the issue why the Maquis was created to begin with? After the Dominion War, what's the reason the Maquis wouldn't be rebuilt?
The Maquis existed to fight the Cardies harassing them in the DMZ. After the war, there is no DMZ and the Cardies would probably either be gone or in no position to keep on fighting. The Feds would be willing to let the Maquis do whatever they wanted as long as they weren't harming anyone.
One of the many things Voyager didn't dive into, even though it should have. Did Chakotay, Torres, etc... all forget why they joined the Maquis? What would they do after they returned to the Alpha Quadrant?
They joined the Maquis to fight the Cardies, and some just were Mercenaries in it for the fighting and didn't have any ideals. Problem is, that doesn't mean much when the DMZ and the Cardies were 75 years away. There wouldn't be much point in fighting the Fleeters when the Fleeters weren't even their real enemy (the Maquis didn't want to fight the Feds if avoided, and the Feds didn't want to fight the Maquis unless forced into it).
Why didn't they care more about their fates back in the AQ? They were too busy surviving day to day to worry about that, and if it came down to it they might've just asked to be let off when VOY was getting closer to home. As it is, they participated in enough good acts that the Feds would be fine pardoning them for any crimes they committed (and they weren't even a particularly violent or criminal Maquis cell).