I think their intent is that the secrets will either be found by other people (even if it's 1 in 100,000 by sheer accident) and then the info will spread. Or you'll end up finding out from the guide.Of course there's some stuff that then stays hidden for years in spite of that, like the sidequest at the end of FF9.
I don't think any of this is a problem. It gives games a realistic feel of depth. It creates an important distinction between a world that's revolving around you as a player and a world that you just happen to be exploring.
A reviewer once said something that really stuck in my head: The greatest fictional worlds are those that feel like they existed long before you were there, and will continue to do so long after you've left.
(P.S go and play FF9)