I personally think that there's no good evidence out there to support the use of ACV. Lots of people are sure that it's a cure-all, but please do your own research to your own level of comfort. People talk about it "acidifying the system", etc, but a normal body (human or chicken) takes care of its own acid/base balance without the addition of "acidifiers", so there's no reason to add it to a system. In humans, you can acidify/alkalize urine but not "the system" with some foods/additives; intake doesn't change the acid/base balance in the body significantly. If you chose to use ACV after your own research, don't use it in galvanized waterers, as it can release excessive zinc into the water from the galvanizing process. Life processes can only occur in a very narrow range of acid/base balance, and adding acid to diet does not change the acid/base balance of the body as a whole.
As far as "natural" ways to treat your flock, do look into dry DE in bedding to help prevent external parasites, though, in lieu of sevin dust and other pesticides which make their way into the chicken, their eggs, and you. Food grade DE is a great alternative to pesticides for external parasites; it is used in the bedding/coop as a loose powder. It works by nicking the exoskeletons of the mites/lice/fleas and causing them to die of dehydration. There is no good evidence that is works as an internal wormer, despite many claims otherwise.
I know I've just invited a huge war here, but wanted to add a voice of reason to the ACV + DE debates.