Ok, let me try to explain it as best I can. Imagine Breaker does not nullify souls/mana/lifeforce when they're in a normal state. You know, chilling and shit. No fancy magic or whatever supernatural power being utilized. For leylines, well, they're basically just holes in the ground and/or terrain. Touma can nullify the conjugation of power/mana at those leylines, but to mess with the leylines themselves would require him to alter the terrain in some fashion. ..is that a satisfactory enough answer for your question?