This is what makes root, or in this case, overclocking that much more interesting. Doing any kind of 'hack' to your phone runs the risk of just bricking the item. The fact that you mod your phone allows you, the user, that much more responsibility and control over what your phone can do or how it can perform. Through stock settings, your running the phone with just that less of a risk of doing any internal damage... having had said that;
Overheating does occur, this is when your responsibility and control over your phone kicks in- you need to be able to use it properly because only you can tell what is good or bad for it. Using it excessively and just being careless with the performance you put it through, causes you to run a higher risk of any internal or, if any, physical damage to it.
This is why disclaimers are placed at the end or beginning of the guides in this forum, not just only to protect the authors but to remind you that you have now access full control over how your phone runs.