First, the system is entirely manual, making it immune to the sorts of technological attacks that make modern voting systems so risky.
Second, the small group of voters — all of whom know each other — makes it impossible for an outsider to affect the voting in any way. The chapel is cleared and locked before voting. No one is going to dress up as a cardinal and sneak into the Sistine Chapel. In short, the voter verification process is about as good as you’re ever going to find.
A cardinal can’t stuff ballots when he votes. The complicated paten-and-chalice ritual ensures that each cardinal votes once — his ballot is visible — and also keeps his hand out of the chalice holding the other votes. Not that they haven’t thought about this: The cardinals are in “choir dress” during the voting, which has translucent lace sleeves under a short red cape, making sleight-of-hand tricks much harder. Additionally, the total would be wrong.
The rules anticipate this in another way: “If during the opening of the ballots the scrutineers should discover two ballots folded in such a way that they appear to have been completed by one elector, if these ballots bear the same name, they are counted as one vote; if however they bear two different names, neither vote will be valid; however, in neither of the two cases is the voting session annulled.” This surprises me, as if it seems more likely to happen by accident and result in two cardinals’ votes not being counted.
Ballots from previous votes are burned, which makes it harder to use one to stuff the ballot box.