Please, don't speak on things you clearly have no clue on.... Overclocking does not put the CPU in a "perpetual high" state. This is not a PC from the 1990s, when overclocking meant the CPU ran at the highest frequency without rest. Overclocked N900s (and even PCs these days) spend lots of their time at lower levels, and only use top speed when doing real work. Most N900 spend lots of time at 0Mhz, the resting sleep state that they all enter when there's no activity. (You can see for yourself, by using this script on your own N900.) Again, overclocking could never cause this. If the CPU ever got hot enough to do this type of damage, it would have already fried itself and the much more heat sensitive LCD layer between it and the screen cover.

To the Op: If you're able, it may be worth removing the flaking cover skin (which has a high chance of breaking the touch screen, so be cautious) and putting a protector on it. It may be worth trying a wet-apply screen protector instead, like Skinomi, since it may mask some of the existing flake in the current cover. I put a Skinomi on mine after the first set of cheep stick-on protectors peeled off. It has a slightly different feel, but is quite nice, and has a rather interesting "self-healing" property. (Something to do with it being a polymer that reacts to oils from the skin... so says a chemist friend of mine.)