Have you looked at Liz Castro's book _EPUB Straight to the Point_ ? It's excellent, especially for iBook publishers. You can find it at her blog site
http://www.pigsgourdsandwikis.com/
I think it discusses the thirty or so available fonts and how to use them, but not the character coverage of each font. One hopes that one of the fonts gives fairly complete Unicode coverage... Perhaps a search at support.apple.com might help (not likely, though)