Still, as much as is practical, we should try to avoid throwing physical documents out even if we know they have been scanned.
I’m not saying that computers manuals will for sure stand the test of time for a the thousand years to come, but as long as they are protected from fire, they are probably a more reliable storage than a digital scan which will need humans to backup them regularly if they want to survive their physical media.
Sure digital backups, especially of PDF files, are easy and cheap, but they require an active human effort to keep the system alive.
Sometimes you just don't need a better scan, because you're just doubling up on data you already have.
With a sufficiently robust QA process, you may be able to catch most of these issues. However, you can never reduce the probability to zero, and people scanning old computer manuals don't always have the necessary resources to implement the most robust QA process.
Meanwhile, mint-condition, shrink-wrapped Magic the Gathering cards sell for $$$. Same goes for other collectibles and real art.
Comparing a periodical to a mint shrink-wrapped MTG card isn't really a fair comparison. Even back in the day, most libraries didn't keep periodicals, they were "scanned" (photographed) onto microfiche at the end of every year or two to save space. Some stuff just takes up too much space to store, or isn't practical to when the information is of limited value or already present in another form.