A Traditionally, hobbyists have not requested permission to designate a real horse as the sire or dam of a model. For the purposes of pedigree assignment, real horses are considered "public domain," and anyone may use them if enough information is available to determine that the horse could have sired a horse like the model (the right breed, age, and color).
Breeders find real horse parents in a wide variety of places. Probably the best sources, if you can find them, are old breed magazines. These are usually filled with ads of horses old enough to sire breeding age adults, and often have articles on bloodlines found in the breed. Another source is more recent breed magazines. Although many times the horses advertised are too young to sire good "breeding stock" models, they are useful for younger models. The most frequent problem with magazines is that ads often do not include foaling dates, and mares are less often advertised.
Another source is stud books. These list all horses registered in a given year or set of years. Not all registries publish stud books, but if they are available, they make an excellent investment for a breed you have a strong interest in. Unfortunately, you need a complete set to trace extended pedigrees, and in some breeds this can be an expensive option.
Also helpful are breed books, breeder's sale catalogs, newsletters, and registry yearbooks.