The iBookstore Formatting Guidelines of September, 2014 lists books in these languages as not yet eligible for distribution: Amharic, Arabic, Aramaic, Burmese, Persian/Farsi, Hebrew, Khmer, Lao, Malay (Jawi/Arabic), Sinhala, Tamil, Urdu.
My guess that that Arabic, Hebrew, Aramaic, Persian, Malay, and Urdu are excluded because the iBooks app does not yet support the right-to-left page turning they require. Burmese and Lao could be because proper line breaking is not possible.
From a separate list of "supported" languages it appears that in addition no books in other Indic scripts are currently accepted -- Devanagari, Gujarati, Bangla, Gurmukhi, Kannada, Malayalam, Oriya, Telugu.
It's not clear why Indic scripts and Amharic are not accepted. As far as I know Pages and iBooks Author support composing in them, and the iBooks app can display them OK.
Edit 3/20/15: I have evidence that at least one Devanagari book has been accepted in the iBookstore.
Edit 12/17: The 2017 edition of the Formatting Guidelines does not change list of unsupported languages.
