Loan secured by mobile home and land. In addition to a mortgage deed we also have executed a security agreement for the mobile home. I feel that document falls under the "security instrument" definition and would require both Lenders and MLO NMLS. Agree or disagree?

Yup

In this instance of a mobile home and land, we would have the above mentioned documents (mortgage and security agreement) as well as filing a title on the mobile home. Would we be required to put the number on the title as well?

The title is not a security agreement, although your interest in the MH will be noted on it. My answer would be no.