In fact the problem with synonyms is not seam-gen, but the hibernate tools, I don't know what database are you using, but I have this synonym problem when I use Oracle.
I think that the trick to solve this problem must be to improve the OracleMetaDataDialect (or the MetaDataDialect for you database) and make it
synonym awareif you do that, then Hibernate and Seam-gen will both be able to generate CRUD screens for you synonyms.
So... I think this is more like an HibernateTools bug (missing feature?)... (no a seam-gen bug)