Also, what should I read to understand the Spanish encomienda system and its successors better?
It would have been a thousand adult males. That makes it a bit harder to determine the total number of indigenous families since unmarried men and married men counted the same. Usually the average is 4-5 people per tributary indio.
The classic text would be The Encomienda in New Spain by Leslie Byrd Simpson. You can also look at Rebecca Horn's Postconquest Coyoacan it also has a good deal on labor relations.