When I started my goat herd, all of my goats were registered, but after a while I realized that it just wasn't worth registering them. It didn't allow me to sell my milk for more money, and I had no trouble selling kids that were not registered. I got a little less for the kids, but it just wasn't worth the trouble of registering them. So, when I bought more livestock, I cared more about the condtion of the animals I was buying, and the consition of the herd that they came from, than whether the animals were registered. However, if you intend to show the animals, they need to be registered.
I think it depends on what you're planning to sell and how much money is at stake. I'm not keen on buying anything that is unregistered except for chickens. All of my cattle are registered, but that's the norm. My goats are also registered, but I know plenty of folks who don't care about that. I think it's a bigger deal in Texas. I have all Rhode Island Reds as chickens, but none of them are registered. I tried to go with what they call the "old-type", because that's what The Livestock Conservancy said was most in danger of dying out. They aren't fancy show birds or anything like that.