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They're files (~ chapters, sections, portions) inside the book that may be skipped when just paging forward/backward. "May", because that's up to the reading application to implement or ignore. The content in those files is still accessible, possibly through hyperlinks, or the TOC. Typical use case are (book- or chapter-) endnotes. You want to be able to see the notes when you so decide, but you probably don't want to page through 10 pages of bibliography references after every chapter.
The "Hide non-linear fragments" option does that. If the books has any such "fragment", it will hide them from normal page forward/backward (and total page count).
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