I've seen the option to put a deposit down a few times. I don't know what conditions must be met before that option becomes available though. I'm guessing location is a key factor. It warned me that if I did it then I had to cancel the reservation more than 24 hours before the pickup time or else my CC would be charged the deposit amount if I didn't show up.

The point of putting money down is to hold your car and telling someone else who reserved that same class that they are out of cars instead of giving them your car because they were there first. But mistakes can still happen, and probably have (I think I read about such an incident on the forums here about a prepay).

Likely, the biggest reason for them running out of cars is because they allow people to reserve cars that are due back by the date they reserve, But then the person renting the vehicle extends their rental and Hertz ends up short. The only way to guarantee that they will never be out of cars is to disallow rental extensions. When they are short because of rental extensions and everyone has a reservation, who gets the car? The person who gets there first.

Edit:
Another reason could be because Hertz just keeps taking reservations until they physically have no cars on their lots? I remember the one time that they were out of cars I could still reserve a car for that day. Until after I complained to them when they called me to tell me that they only had a compact available instead of my premium. Then when I looked on the website after the call every single car from the HLE and SRQ was unavailable, even though all of them were available not 60 minutes prior. (I was doing last minute rate checking) I basically gave them the Seinfeld speech that you posted above. I love the end of that BTW.