Shot holes can be made by a number of things. Shot hole fungus is another besides Bacterial Spot. it is most likely bacterial spot. The most effective treatment is Oxytetracycline. An antibiotic which you probably cannot get without a pesticide license. Captan and copper are your other alternatives but only give modest control and can damage leaves big-time if misused. You should always spray copper on peach trees 2-3 times a year when dormant. You're in CA so Valentine's Day, Christmas and Easter are the best times. You can spray now but need a small dose. You also need a sticker. Bacterial Spot can spread unto the fruit too.
http://msue.anr.msu.edu/news/managem...and_nectarines
The best copper product to use is Kocide, and use Nu film 17 a a sticker. If you want to use the very best sticker and the strongest copper and most effective. You will have to purchase online. Dose for Kocide is 2tb per gallon. Since it's give per acre, you might need that info.
If your peach is O'Henry for sure it is Bacterial Spot as it is a magnet for the disease. Too bad as the fruit is outstanding. One of the best!