I agree with bobcat that it depends what type of hole as stretching can make it worse. With fox/yotes you can sew a lot of holes that don't show up as they are turned fur out and the fur hides most of the sewing typically. For coons, rats etc you can sew little holes but the big ones are too obvious. I normally still sew them because I'd rather take it sewed then with a big hole. Now if you take your time skinning and especially fleshing you should be able to avoid most holes. Good luck!
As far as getting docked for the holes it all depends where the hole is. For coons they typically just use the fur on the back so if you get one on the belly it might not be as big of a deal. Still sew it up and make it look as best you can.