Horses, and livestock in general, do become accustomed to disturbance. Here in the South of England, where helicopter low flying is a normal everyday occurrence, horses and other livestock quickly get used to the noise.
The one thing that I know really does spook even a well-acclimatised horse, is the sudden arrival of something noisy. If they hear it coming from afar, they seem not to be particularly perturbed as a rule.
We've lost livestock (cattle) from being spooked. They've run into fences en masse and suffered severe injuries, usually badly torn udders from running into barbed wire. The main culprits have been very low flying military jets, which appear to come from nowhere, although the occasional very, very low flying Chinook has caused the odd problem.
Generally, if aircraft stay above about 1000 to 1500ft I really don't think most animals will be too bothered, although I certainly believe that we are well-advised (in the interest of being good neighbours) to keep as far away from livestock as we reasonably can.
VP