Here are some ideas:
Some compound nouns do not use hyphens and some do. Unfortunately,
there is no definite rule to follow when it comes to hyphenating
compound nouns. The best way to decide when to use a hyphen in
compound nouns is to look up the word in the dictionary. If the
compound noun is not found in the dictionary, most often the words
should not be hyphenated. If the dictionary indicates the words
should be hyphenated, then make sure you hyphenate the words. Ex.
Obtained from here: http://www.uhv.edu/ac/grammar/pdf/hyphens.pdf
This site lists a number of standard dictionaries that use the e-book version, but counters it with the widespread use of eBook in the publishing industry: http://www.dailywritingtips.com/ebook-ebook-ebook-or-e-book/
We do not normally say e-mail (at least not any more I think), so it seems it is mainly a matter of choice. There does not seem to be a standard yet, and it may be spelled ebook or e-book as per the user's choice, while eBook seems to be wrong and only used for aesthetic purposes in marketing.
For this website I would prefer using the non hyphenated ebook version, as I am sure many users here will need to browse the site on handheld devices besides computers, and it is difficult to put in the hyphen, especially on smaller screens. When the same idea can be propagated with less number of keypresses, why use the longer version?