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I don't think font embedding will prevent the book from working in any reader, at worst, the embedded fonts will not work and default fonts be used.
The main "problem" is InDesign will probably encrypt the embedded fonts. There are currently two methods for encrypting fonts in ePUB, one is suported by the official specification, the other is used by Adobe. If the generated ePUB uses the second method, it won't be standard-compliant, but it will work in ADE-based readers.
As for whether it's better to embed or not to embed fonts, I prefer not embedding them, at least not for the main text, so that the user can choose his preferred font. For some decorative or special purposes (titles, blackletter fragments, pieces of handwritten text, etc.) embedding is fine
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