True about that, but that has more to do with shrink wrap, not properly sized resealable baggies. Re-shrink wrapping stuff is not a good idea for some of the reasons you listed. When I've bought japanese things, they usually came with a resealable baggy, not that shrink wrapped shit which is often the case in JP stores. If your games smells, it is already FUBAR'd in my opinion.
I honestly doubt condition was why they didn't seal famicom/sfc/neo geo games etc. They probably saw no reason to do so compared to here in the States/EU where people steal far more often than there. But yeah I agree its dumb to shrink wrap AES games for example, especially if snaplock cases as the potential for insert indentation damage is quite high.
I thought we were talking about resealable baggies, not re-shrink wrapping stuff. On sealed SNES/N64 games ive opened the shrink wrap has done no damage, in fact its protected it. It isn't like LPs were the corners can get damaged over time due to the shrinkwrap shrinking. I will say this, those baggies are not going to protect the game from REAL damage such as a fall or indentations like a soft plastic case would. Resealable baggies are a godsend for steelbook games and dvds, cds. For my boxed games I just use those plastic boxes that fold up, acrylic case if its an expensive one. Like the resealable sleeves, they are acid free and provide quite a bit of protection. Air is still getting to them at a much lower rate than bare, but allows them to breathe. You find this problem a lot when people frame anime or cartoon cels in a sealed environment to display, the chemical reactions in the paint and paper has nowhere to go and starts deteriorating itself.