i think it has been proven that the deeper you go, the less importance that is assigned to the page, etc.
grobar - That really is about click depth and linking structure, not directory structure, and it comes from the way that PageRank is divided up among outgoing links from a page.
In the classical (read, slightly dated) view of PageRank, the PageRank conveyed by each link on a page is equal, and if there are N links on a page, each link transmits 1/N of the total accumulated PageRank the page has to transmit.
Assuming "top down" PR transmission (ie, thinking only of PR transmitted "down" through a site via a linking structure from home), as you go down in a hierarchical linking structure, the PageRank is increasingly split up from level to level.
A direct link from top level page carries more weight than a link from a page lower down in the
navigation hierarchy, because the PR from home hasn't been split up the way the PR from a lower level page has been split. This is regardless of how the pages are organized into directories.
There are a lot of nuances to this, as well as considerations of how PR circulates throughout the site, but that's basically it.
The confusion between directory structure and navigation structure has come about because sites with hierarchical navigation are generally organized into directories as a convenient way of keeping things straight. There's nothing, though, that says, though, that any pages in such a directory structure even have to link to each other.
I'll let someone else tackle siloing... and I don't think you're going to get a reference, though. Wikipedia is probably a good place for that.
But, IMO, if you wanted isolation between various types of literature on a site about books, directories as you (only partially) describe provide a good visual basis for thinking about organization and keeping your pages straight. You still need to create the links within that directory structure.