The whole "They're living ships, they can self-repair" thing doesn't really hold up. Even if they are organic, then they'd need to eat stuff to get energy to power their "healing factors" the same way we have to eat to live and power our own "Healing factors".
Voyager has replicators, including Industrial Replicators for Engineering and stuff. They should be able to absorb the raw energy from...virtually anything in space (Suns, Nebulae, random space radiation) to power the Replicators meaning it has just as much a "Healing Factor" as those Living Ships.
So why does it not get this pass that they do?
The Destiny in Stargate Universe was out in space for millions of years and yet it needed no maintenance to function after that time, no one complained there either.