I have a theory about this.
Voyager wasn't just looking for Chakotay's Maquis ship because Tuvok was on board. There were bigger things going on.
The official number for Voyager crewmembers when they started their mission was 141, including Paris but not including Tuvok.
However, when I started to count crewmembers who are mentioned in episodes and books I came up in 184.
And that's without Chakotay's Maquis crew who were 31 people mentioned in episodes and books, Tuvok and later additions like Neelix, Kes, Naomi Wildman, Seven, The Equinox crew, and the Borg children.
So why are there more people on the ship than the official numbers states?
My theory is that Voyager wasn't just looking for Chakotay's ship. It was also about invading the Maquis controlled planets in the Terikof Belt.
The Voyager crew was about 140 people, then there was a special task force of 33 people whose orders were to establish a bridgehead on one of the Maquis-controlled planets and from there bring in more Starfleet ships and soldiers to conquer all Maquis-controlled planets in the area. Lt Commander Cavit would have been in charge for the task of conquering the most important Maquis-base in the are and establish a bridgehead there.
Therefore the ship was commanded by a captain, in this case Janeway!
Due to the delicate details about this invasion and to avoid that spies would find out about the mission, the whole thing was kept secret. Only a few people, including Janeway, Cavit, Dr. Fitzgerald, Chief Engineer Honigsberg, Tuvok and the task force members knew about the mission.
However, as we all know the plan was never sat in motion due to the fact that The Caretaker transported Voyager to the Delta Quadrant. Since Cavit, Fitzgerald and Honigsberg were killed during that event, Janeway and Tuvok were the only survivors among the senior staff who knew about the secret mission.
When Chakotay and his Maquis crew became members of the crew, Janeway decided to keep the secret mission a secret. The reason for that was that if words about the mission came out, it could create more tension between the Starfleet crew and the Maquis crew, something that Janeway wanted to avoid at all costs.
And if the crew managed to find a wormhole which could take them back while the Maquis still were active in the Alpha Quadrant, then the invasion plans could be an option again for Starfleet Command and in that case it would be better if so few people as possible did know about it. Therefore the task force members were ordered not to reveal anything to anyone about the mission. Instead they were transformed into ordinary Starfleet crew members with the one and only goal to find a way back to Earth.
As the time went by, the mission was soon forgotten by most people involved. It's possible that Janeway informed Chakotay later on about the original mission but for most of the crew members it remained a secret.
