[Q]

Even if the AI claims the empty system, the AI will never claim the next adjacent system with planets next to the empty system. Therefore that will stop it's expansion if I prevent any colony ship to get there (which is quite easy).
The refuel of colony ships is indeed not a too big problem. I myself posted standard colony hull ships with a quantum reactor for the late game. But in my experience in the early to middle game even the "advanced" colony ships with light cruiser hulls and supply storage components run frequently out of supplies. And because the AI builds it's colony ships mainly on the home worlds in the center of it's empere (which is good, because there is enough population) the way may be too long without resupply.