I prefer to believe that the Shivans didn't make nodeless jumps during the Great War, rather they used nodes that the Terrans and Vasudans didn't know about and still don't. Perhaps they were low-stability nodes and resided below the detection threshold of the sensor systems available to the Terrans and Vasudans.
In regards to the Capella incident, I see it two ways. The first, is that when the Saths jumped out, they were merely jumping to another location within Capella to avoid the shockwave. The other is that the supernova did something to local subspace, opening some kind of rift that the Saths were able to jump through. It would seem to fit with the general notion from the final cutscene, where Petrarch speculates that the Shivans needed to destroy the Capellean sun to get home. Its the general belief among the community that there was more to the triggering of the supernova than a simple weapon of mass, mass, mass destruction.