Not sure myself about the current line-up - but with previous releases some heat was designed to be dispersed via the keyboard I believe. However I think this was negligible, or else the iSkin and others like it wouldn't be so usable and popular.
I think the benefits of using an iSkin outweigh this possible risk - just my opinion.
I know sometimes it feels like the computer is sucking air in from underneath the keyboard, because it feels like cold air is being sucked in from the top (makes more sense then how PCs do it from underneath the machine).
But I guess Apple Stores would not sell the product if it interferes with the computer's cooling.