I guess it depends on what you are trying to do with a fuge. I use mine to grow algae and my mangroves. I put a regular grow bulb over my fuge which causes algae to grow like crazy. I figure that if I have algae growing in my fuge, it will not want to grow in my main tank. I then just scrape this algae out every now and then when I feel it is getting too thick. It kind of works as an algae scrubber which increases dissolved oxygen and it removes phosphates and silicates from the water. I also like to keep my heater in the fuge because I don't like to look at it in the main tank. I put the heater in the fuge and the thermometer in the main tank. I then set the heater so that it maintains a tank temp of about 82 degrees. If you want to keep fish in your fuge then maybe putting your heater in there would be a bad idea since your fuge would probably run a few degrees warmer because it is heating up your main tank.
Either way, I don't see a problem with using diagonal baffles. It just depends on wether or not it will work for you.