The thing is, you're dependent on the Jump Node network. For example, imagine that in order to get to a Star that is 20 Light years away using the Subspace Node system, remembering that the Nodes seem to find their exits almost randomly in real-space terms, you could find that you have to travel through hundreds of unpopulated systems to reach it.
Now, assuming the Shivans are a 'reactive' race, the story of Freespace 2 suggests that the Shivan fleet responded to the incursion in the Nebula. Either they had 80 Juggernauts in the area, just in case, or the Fleet mobilised very early in the campaign, possibly as soon as the Shivans were aware of the NTF in the Nebula, I'm not certain of the time frame of FS2, but I get the feeling the gap between the NTF entering the Nebula, and the Juggernauts arriving was around 8-12 months.
I start veering more into theory here, but we have to assume that 80 Juggernauts is not a small investment of resource, even for the Shivans.
So, you have a race that has a massive fleet that responds when they encounter a new enemy, you can even fit the Lucifer 'Scout' theory into that. Even with 20-30 Fleets of the same size in operation, the odds of the Shivans being able to track down every inhabited system that is connected to an enormous jump-node system (particuarly for races that can stabilise weak nodes) is extremely small.