So I just mailed to the inventor of JSON Schema.
If URI References would not be allowed that would also mean that many implementations have to update their code,
for instance heroku or jayschema, saying
"
Format specifiers
• uri: As in RFC 3986 Appendix A, including relative URIs (no scheme part, fragment-only), with the exception that well-formedness of internal elements, including percent encoding and authority strings, is not verified.
"