Well in our game we have both of the last core reactors on different parts of the galaxy. The other one 9 hops away and the other 5 something.
If they are both Group A Core Shield Generators, and they truly are the last two, then you'll only need to hit one of them. The last one will self destruct. If they are from different groups (non-A Group) then you'll only need to hit any one of the group and the rest in that group will self-destruct. If both CS Generators are from different groups, then you have still more Generators on other planets that you haven't scouted yet.
And to top that, both homeworlds are right now about 10 hops away, each in totally different direction. Right now we have about 25 planets.
Yeah, I think it's an intended feature of the game that AI Homeworlds spawn just about as far from the human Homeworlds as is possible.
So how do you guys usually deal with far away core reactors?
There's no really easy way to do it unfortunately, since as you know, you'll need to build a Command Station on the planet in order to destroy the Shield Generator. If the planets are on systems that are a long way from the AI Homeworlds, this can work in your favour by bluffing the AI into reinforcing worlds that are not really tactically important to you.