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Hmm, it's a tough choice. Currently as far as I know, UUIDs are used in only two places (the OPDS feeds generated by the calibre content server and to set the identifier for a book when converting it to EPUB). This would break the second, but not catastrophically. On the other hand, altering the schema to add a remote_id column wont break anything catastrophically, since the only code that would depend on its existence would be the downloading code.
Looking at it from another angle, do you really need to put this info into the database? If instead it were stored in a config file as a list of previously downloaded urns, it would server the purpose of avoiding re-downloads. You can use the XMLConfig class to achieve this conveniently, it will automatically serialize a python dict.
If you do intend to do a browser eventually, let me know as I'd like to abstract its design to support sources of books that dont export OPDS feeds, like MobileRead.
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