Cornelius, the discs I have that did not originally have pinholes worked for years. Now, after the pinholes, some do not (and the ones that do, most of them I have not played all the way through to properly test them.)
So, it can and sometimes does create enough loss of data to be unplayable or at least effect the game (freezes, lost audio, etc.)
Rarebucky, I have noticed the clouding issue on Saturn games also. It seems to be the same issue you are describing. I also noticed a few Sega CD games with similar splotches. I'll have to research my collection and see if any of the clouded discs were purchased new.