Something to keep in mind is that printed, government-supplied ballots happened relatively late in our political process. In 1860, one would vote by writing out a ballot for a candidate or slate of candidates, or alternatively by using a ballot that was printed in a newspaper or similar publication or handed out by a candidate's supporters at the polls. So Lincoln not appearing on ballots in the South is fairly normal; he was so unpopular there that few people would have dared to write him in or publish a ballot for him.