It reacts with the metal.
How fast depends on the metal as it is only a weak acid. If your waterers are gold it is probably OK to use vinegar! Vinegar will react with zinc - which is commonly on the surface of animal products as 'galvanized metal'.
Zinc in excess is toxic to chickens and the vinegar will strip the zinc off the galvanized surface and so the zinc will be in the water the chickens drink.
It will also rust iron and low grade stainless steel potentially as well.
This doesn't happen instantaneously - vinegar is already a weak acid and it is only a weak solution being used for the chickens - so a weak solution of a weak acid. Flushing with vinegar to clean stuff shouldn't be a problem for example, but using a metal waterer (or nipples) and having them sit in vinegar day in and day out will eventually cause them to corrode.