I have to imagine the creators of these sites built a mechanism to detect "Vote Fraud". Is there something to stop someone from creating two accounts and continuously vote for each other to build reputation?
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Basically SO query the database from time to time and if they find that a user is just upvoting some other specific user, they all the points from that user are removed.
This is called sock puppetry, and yes, there are tools to prevent it and appropriate recourse when it occurs.