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?
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?