You have the fuel and other resources to travel to your operational range in one step, even if that step takes a year or more. There's no intention that ships will fail to reach their destination - travel is pretty much a sure thing, not something that too much game time should be spent on. The worst you can do is have a really bad journey. After all, the fun is at the destination!
So no, there is no limit other than the ship's operational range in terms of fuel. Like you say, they can get rough if you fail all the checks though (and bear in mind that failing the navigation check doubles the cost of fuel, so that could cause real problems!)
If your PCs really do insist on a single long journey, you can always spice it up with a shipboard adventure to pass the time. Or just skip ahead and tell them they arrive 5 years later, weary, and aged a little (depending how far they go).