They've already moved on to genetic engineering according to the article; no need to fuss with evolving a better horse when you can directly specify one.
At some point breeding programs will mostly be useful for identifying new mutations to splice into the main branch.
Funny that despite Neuromancer's prophesying the ubiquity of gene-splicing in future culture, William Gisbon specifically discounted it in this instance. As per the Finn: "Arabs still trying to code 'em up from the DNA, but they always croak".
At some point breeding programs will mostly be useful for identifying new mutations to splice into the main branch.