Three-nacelle (trireme) rigs are probably the exclusive province of long-haul operators, where endurance and reliability are valued over speed. Possibly also solitary deep-space survey missions, where there is no Federation depot to pull into and repair at. In my headcanon, the two DS ships that were diverted to rendezvous with Voyager were triremes, probably something based on either the Excelsior or Enterprise-B hull frames -- but were never seen onscreen because Janeway found the Borg transwarp corridors and with some futuretech smuggled to her by her future self, got the rest of the way home in one jump.
