I would say "A transfer letter was issued to Ann, with John & Mark as signatories".

The second sentence is correct. "Signatories" means one who signs, which often implies on contracts the one who is agreeing to the contract. In the first sentence, it would make sense to write, "The transfer letter was issued to Ann with the signatures of John and Mark." "Signature" is the signed name of a person, showing agreement or authorization. Note in both sentences, it would be better to write, "The transfer letter...".