Re: Advantages of hand-marked, paper ballots
The meatsacks are easier to "hack" one-on-one perhaps but it does not scale well at all. However if you hack the hard/software once, you can hack them all. This scales in a way that meatsack fiddling does not.
Missing ballots, again, does not scale well. It can become obvious that things are missing and recounts/revotes taken. If you hack the hard/software no vote is missing, you simply alter it to what you want. This is much harder to spot.
That said, mail voting is the most likely form of meat-space voting to be fiddled with; often in places of multiple occupancy where one person can collect the ballots and vote on them all. This happens in some communities more than others.