When it comes to the display of text in your re-flowable eBook, you have a some choices about hyphens.
Some general points
Hyphens can be useful to break up long words across the line break. This is particularly appropriate if you want to justify your text, since the renderer will need to space words out, and this can lead to uncomfortable spacing! But you need to adhere to the following rules:
Don't justify headings. This is because they may not span the line, and so you are going to get horrid space between the words.
Don't hyphenate the headings
Don't justify your verse
Only hyphenate if you are justifying the text and the line width (measure) is relatively short.
In the iBooks app on the iPad the user has control over the justification. Well, that is, by default justification is turned on. Users can turn that off - but they probably don't! ‘cos they don‘t know where to find it.
How can eBook designers get the kind of alignment they prefer, and make the eBook stay like that?