Why do people want the Yor repeating the Matrix? Or do you want the Yor livestocking ignorant humans? Which is it? Do you know the amount of energy that would waste? The Yor aren't retarded, unlike the premise and the "science" of Matrix.
The Yor can go out and harvest all the hydrocarbons they want from any source of normal matter! That's nebula, worlds (rocky and gas giants), comets, asteriods... everything in the universe! Why would the Yor bother to "husband" any living creatures, when they can just process the entire universe into base material and fuel? Answer: They wouldn't. Only some left over "caretaker" prejudicial order or ancient memory from when they served their creators could possibly get them to forgo efficency for "pet keeping". And they aren't going to let that get out of hand... it isn't efficent.
The Yor can do things we could never do. For instance, the Yor could harvest all the frozen methane located in the sea floor on Earth (see:
Link), and never worry about the destruction of the world environment using it would unleash. They could drain the Earth's oceans, using a bit of solar power as the seed energy to split up all the water into Hydrogen and Oxygen, and burn that Hydro! They could move the Earth 50% closer to the sun, so that solar power systems could provide tremendously more power from the big fusion engine in our sky! We couldn't dare, but the Yor? Their survival is not constrained to the same narrow environmental envelope that we require. They might prefer Earth type worlds for easy access to resources and the low cost of maintaining their physical bodies on such worlds, but it isn't the only option available to them.
Remember, whether it is using humans or cows, it is still a matter of economics. We continue to use cows because there is a market for the meat and cheese and leather (and everything else we use them for). But if the economics turns against it we will stop. If it was cheaper for us to mix a few chemicals in a big vat to produce the meats, cheese, and leather equivalent, without wasting all the time and land and energy on raising the cows, we'd switch to that. In the long term, economics determines the behavior of a society. The Yor would never use organic life as their fuel, unless that was the cheapest economic source of power available. As long as they have access to hydrocarbons, it isn't. As long as they have access to an ocean, it isn't.
Note that. You want the Yor growing pigs and using the pigs and their wastes as power? Then you have to make the economics for that work better then everything else available to them. Consider, we could power the world right now purely on corn, but we are not. Why? Economics. It's cheaper to go drill in the ground and use that (the oil and natural gases) then it is to grow all the corn and process it into energy (even if its just collecting all the husks and burning them!).
Reusable isn't more efficent. "Reusable" implies sustainability. But if the economics doesn't support sustainability, you will not choose a reusable methodology as your primary means of powering anything until it is more economical then the alternatives.
What's the cheapest source of power? Harvesting sunlight. The star is releasing free energy, and there are mydrid of ways to convert that output into useable energy. Heck, to harvest the power of sunlight, you could just use long metal poles with wires attached at either end. With one part of the pole "closer" to the sun, this will create an electrical current when the sun warms the pole. You cannot beat that for "efficency" (cheapness). It works so long as there is light. No muss, no fuss, no having to worry about keeping your organics alive and healthy, and then process them into a fuel later. The rods are generating power, consistantly, for extremely minimal maintainence. They just generate a very low current. Or you can hang out several hundred meters of arial, and harvest ambiant (that means, free) radio waves. As there is always radio waves, this is a power source that works 100% of the time, regardless of if its night or day! But again, this generates a very low current.
Remember, economics. If the economics doesn't favor it, then they aren't going to do it.