Syscoin is a great project. I am an experienced C++ developer and I am impressed with your code in Github that supports Aliases, Certificates, Escrows and the Blockchain market.
I don't think the encrypted messages should be stored on the blockchain. Yes, it is encrypted with a 256-bit ECC key but, IMO, all encryption will be broken one day and replaced with something better so it is not a good idea to leave encrypted data in a public place like a distributed blockchain. Something like MaidSafe's Safe network where the cypher text is cut into many pieces and distributed offers much more protection.
Yes you are right there is a path fwd for messages using ecdh with ecies so message is authenticated but offchain.