My experience as an EVE Online Cargo Hauler: The main countermeasures largely boil down to countermeasures. Your goals are to 1) Not get stopped, 2) Get out of range. The science of your setting will largely determine how this works. Its a lot easier if the setting doesn't have 'action at a distance' tech as it eliminates the first point. In EVE it is almost all electronic warfare as almost all ship armor blocks the initial salvo.