Plant breeders, since ancient times, have had to make a decision as to whether it will be more practical to develop a seed variety, or a clonal variety. Breeding clones is easier than breeding seed varieties, but growing seeds is cheaper than clonal propagation techniques like layering and cloning. The decision is generally that if the plant is long-lived (think tree fruits), breeders will go clonal.
Making a moral or environmental issue over it would be IMHO absurd.
As already noted, clonal animal breeding would not be cost-effective.
Re animal welfare, if there were cloned animals, each one would have a rather similar personality. This would affect how stressed AKA unhappy the animal is living in conditions of industrial agriculture. I imagine that some clones would be more amenable to living under those conditions than comparable traditional breeds, and some less.