I was just a kid when I first saw that episode of the Simpsons so I don't really know what work was like at the time so it's possible I just didn't get the joke at the time but I just thought about that episode and frankly it's gotten even funnier because Scorpio is probably the best boss you could get.
He's friendly, encouraging, goes to considerable effort so ensure a positive work and home environment, more than fairly compensates his employees for their labour and even finds the time to personally interact with his employees despite running a worldwide criminal enterprise. He even manages to turn Homer Simpson into a productive employee who enjoys his job. At the end of the episode, despite being actively under attack from the US military, he still takes the time to have a heart to heart discussion with Homer where he encourages Homer to do what's best for his family and not his employer.
Now yes, he is technically a supervillain but is that really so bad? We don't know exactly what he gets up to but think how bad he would have to be to be definitively worse than all real world companies. Think of what companies like Nestle have done or the oil companies or the pharmaceutical industry. Scorpio could start everyday by punching a baby I'd only be comfortable saying he's probably one of the worst people alive today.
It's just really funny/depressing that by today's standards Hank Scorpio could be considered a really good person to work for.