There a standard way to assign (PGP) EPUB eBooks?
A way to use digital certificate, like in the PDF's certificate-based signatures, but not PDF.
Theoretically, you could add a signatures.xml file to the epub. However, I don't know of any epub app that actually supports this feature.
I.e., you'd also have to provide readers with a standalone app that validates the checksums.
It'd probably be easier to generate an MD5 checksum for the whole epub.