yes any sort of insect becomes a problem around flowering time. The only risk associated directly with carpenter ants is their nests will damage root structures. This is more a problem you would find in an outdoor grow, because full ant nests can sometimes span some 10 feet underground. As long as you don't see ants making colonies in your pot and pouring out of the soil you have no reason to believe they have damaged your roots. Your method of extermination sounds slow, but if there is no queen there will not be any more ants reproduced. Good luck, and Jah Bless