The problem with ammonia is that the ammonia gas evaporates out, leaving plain water. Water, of course, promotes rust. The other problem is that copper in a barrel acts as "reverse galvanizing". Where zinc will protect steel, copper does the opposite, and promotes pitting and corrosion. Leaving water in the barrel forms a battery, with copper and steel, and promotes the pitting.
I am trying to remember the downside of ammonia and can't right now. However the word is residual ammonia in a bore is not good - someone else can outline the ''why".