I only notice this on the crappy type of shrink wrapping where it's done on a straight line across the top. That type I do believe squeezes the package slightly. Never seen this problem with y fold seals, although some of them I notice, are more airtight than others. Like for example, I've notice that Nintendo published games tend to have more snug shrink wrapping than others, and the games tend to stay in better condition that way. I've never noticed that it actually causes any damage.
I don't collect sealed games, but some of my games are still sealed.