alt Hacker NewsPaper ballots definitely have security problems too, it's just harder to compromise an election with many polling locations if it uses paper.
E.g., a counter can put a bit of pencil lead under a fingernail and mark overvotes on ballots they don't like, thus causing them to be adjudicated or not counted.
This is in some contexts solved by having different ballots per choice. In Norway you go into a booth and select the ballot of your preferred party, fold it (they all look the same on the outside) and drop it in the box.