Yeah, there are some things in older games that are only mentioned in the manual, yet are considered official parts of the story. I also used to read them for every game back in the N64 days. I still remember reading the DK64 and Mario Party manuals (Cranky being the voice of the manual in DK64 was great, & I always approximate a 20 turn game of the old Mario Party games to an hour of gameplay as mentioned in that manual).
I think there was some value there that can't be found in digital manuals, though the latter are certainly less likely to be thrown out, lost, or destroyed from use.