Evaporation = cooling. Heat is lost through the tank through the process of evaporation. If you leave the glass tops on, you're limiting evaporation, which is trapping heat. I realize that you want to avoid having to topoff your tank regularly, but it's better to do this that overheat your tank. With glass tops, the fans won't do much, since they can't really blow over the water.
Also, where do you have the chiller located? If it's in the same room as the tank, it won't work as efficiently, since it needs cooler air to transfer heat.