In short, the South Korean government considers both North and South Koreans to be recognized as South Korean nationals. Basically, if someone from North Korea manages to get into South Korea, an evaluation can take place to award citizenship.
While North Koreans don’t necessarily have automatic protection, as criminals are not allowed to be naturalized, the bulk of North Koreans that can prove their North Korean citizenship can still be accepted. People can also become South Korean nationals by being born to a Korean parent (if the Korean parent is the mother, the person must have been born after June 13, 1998).
Being abandoned as a child within South Korea is also grounds for citizenship. People can also simply apply for naturalization.