Actually STO is allowed to use everything from XI and Into Darkness, CBS asked them not to use anything from Beyond according to one of the employees from Cryptic. They just chose not to use those ships you mentioned. The Naradra is nearly 5-6 miles long, so it would have been too big. And small shuttle craft like the Jellyfish are not very popular. The Kelvin is also an old ship, but they brought back the NX-Class and Refit as a 'replica', so they could use the same excuse for the Kelvin. AFAIK, that "fact" comes from an often out of context quote from one of the writers. He later said in the same interview that 'canon is up to the fans not him' or something along those lines.