A "deep link" is a URL that doesn't point to the "home page" of a site -- usually, this means contains something more than just a domain name [optionally followed by "index.htm" or the like.] It "addresses some page deep inside the site", not its "main entry point."
A site that has pages (or subdirectories) with information on several different topics might have each such page or subdirectory listed separately (and directly) under several different categories. This would be "deeplinking".
The guidelines say "deep linking is the exception" -- that is, the deep links in a category should be consistently of significantly higher value (quality of content) than the minimum required for a site listed in the same category.
In practice, this means that certain kinds of sites (e.g. online retail sites) are "basically never" deeplinked, while others (e.g., encyclopedias, newspapers, large "conglomerate" corporations, newsgroups or etext archives, universities) are "frequently" deeplinked.