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The answer to that is "it depends on you". I think they should be checked, so I default then to on where I can. The language code sets the book language internal code based on what you see the language as in calibre, the markup cleaning removes things that shouldn't be needed (blank paragraphs, empty div tags, etc.), and the hyphenation adds a CSS file to the book that instructs the renderer to hyphenate words according to the internal language code if it's one that the Kobo reader supports.
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