Different devices offer different fonts, which may not be under the control of the book designer.
The iPad is the most sophisticated tablet that has a lot of built-in fonts, and these are available to the ebook designer.
When exporting to ePub from InDesign you can specify that the fonts are embedded.
InDesign CS6 will encrypt the fonts using a method acceptable for the ePUB3 standard recognised by the International Digital Publishers Forum(IDPF). Unfortunately, the font files are also obvuscated and this is not acceptable to some eReaders.
Naturally enough, fonts embedded from the InDesign export to ePUB3, will display correctly in Adobe Digital Editions. But what about getting these fonts to display on the Apple iOS devices, such as the iPad?
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.