The Eureka Maru has been in the Valentines family for a long time. To some people, it would be described as an ugly, restrictive spaceship but to Beka with its history, its lovely. The Crew use the Maru when they plan to visit somewhere and the Andromeda is not the ideal ship for the job. It has no weaponry so its used sparingly.
"It has no weaponry so its used sparingly." That is a completely false statement. It does not have the combat capabilities of Andromeda,but the show clearly shows that it is armed. In a few shows they even go on to state that they have been upgrading it while it stays on Andromeda.