Unfortunately, this countermeasure was proved near useless when Bulma invented the Dragon Radar, allowing the Z Fighters to easily find the Dragon Balls and summon Shenron many times.
After used to make a wish, the Dragon Balls scatter across the planet, giving them time to dispel the dark energy harmlessly (since it is expected that it would take years for someone to find all the Dragon Balls and summon Shenron again, especially since most people do not know about their power). The dark energy stored in the Dragon Balls disperses only after 100 years, and the Dragon Balls can only store a limited amount of it. To prevent this energy from causing problems, the Dragon Balls absorb this dark energy.
First mentioned by Old Kai in Dragon Ball Z, whenever a wish is made using the Dragon Balls, an equal amount of negative energy is created alongside the beneficial wish-granting energy.