I was putting together a list of the various thematic narrative arcs or 'arc threads' that Voyager dealt with over the course of its 7 seasons, and identified 20 episodes (5 in Season 1; 8 in Season 2; 2 in Season 3; 1 in Season 4; 1 in Season 5; 2 in Season 6; and 1 in Season 7) that dealt, either directly or indirectly, with Maquis-related themes.
For reference's sake, I'm listing those episodes below:
State of Flux
Basics, Part 1
Basics, Part 2
Worst Case Scenario
The Voyager Conspiracy
20 episodes out of 168 might not seem like a lot on the surface, but it surpasses the number of episodes from both TNG and DS9 combined that dealt either directly or indirectly with the same subject.
BTW, the Maquis thematic narrative also has, I believe, the second-most amount of episodes dedicated to it of any of the thematic narrative arcs with which Voyager dealt, surpassed only by the thematic narrative arc/arc thread of Borg-related episodes (of which there were 22)