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As Jellby said, there's a whole issue with font obfuscation when it comes to InDesign. On the whole, though, I far prefer it if ebooks do embed fonts. Ebooks aren't print books, but that doesn't mean they don't deserve to be treated with the same respect and be presented in a font that reflects and enhances the content. It's not a matter of having a 'favourite font', since you should use a different font for setting Tolstoy compared to Roth. But some publishers have adopted the practice of embedding the same rather sub-standard font in all their epubs, and that's certainly a practice to avoid, since it adds nothing to the text.
iBooks doesn't use embedded fonts (and the submission guide states you shouldn't use them), but other readers don't have a problem with them.
The major issue is licensing. The majority of font licences don't allow embedding in epubs, even if obfuscated. One way around this that I saw used in Philip Pullman's latest book is to specify the font in the css, but not embed it, so that it will be used if present on the reader's system.
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