Other than a much slower computer, there is no downside to limiting the frequency. Your laptop will run longer on battery, as it is not drawing as much power. The fans wont spin as often and/or as loud, as they dont need to disappate as much heat. Generally speaking, your computer should last longer. However, in reality, modern laptops are very robust and you shouldnt expect any failures before modifying the CPU frequency.
The real question is what is going on. The turbo boost feature is doing the exact opposite of what you did. It is turning UP the frequency. The advantage is that it speeds up the computer. However, it should only do this when the computer is under heavy load. When the CPU starts getting to hot, it should slow it back down. It really depends on what you consider "uncomfortably hot." Do you have it in your lap? Are the air vents blocked?
Losing almost 1 Ghz (per core) is a massive performance hit. Im genuinely surprised you said you havent noticed it being slower. I can only assume you arent running any CPU intensive programs. Personally, if the speed of my computer dropped almost 50%, I would notice it immediately.