Most “retro” games have been backed up but the definition of retro shifts all the time. You don’t even need to go that far forward: the PS3 and X360 have a ton of missing stuff - games yes but especially DLCs and update versions.

The pre-online era was “easier” - find each revision of a Donkey Kong Country cart and your job’s done. Now, every game has 12 versions and casual pirates that “just want to play the game” only bother sharing the oldest and newest ones. There’s content locked behind promotions and account bonuses. There’s patches that alter or remove content (or patch important speedrun tech out of games). And the presence of online in otherwise single-player games is always going to be something inherently opposing preservation of the original experience - you’re not going to ever get the same experience playing Wind Waker HD with Tingle bottles that I did because either the feature is dead or it’s been reimplemented through something like Pretendo. And with a reimplementation, the source for the community posts is no longer casual fans taking selfies with bosses but instead comprised exclusively of tech savvy users who bothered to install a fake Miiverse on their hacked Wii U / emulator.