does the prepayment penalty need to be disclosed on the loan agreement and the promissory note for a commercial loan? What about on the deed or mortgage?

Just my opinion, but I would think as a matter of contract law you'd want any prepayment penalty dicslosed in the loan agreement (at a minimum).

I would always include any pre-payment penalty language in the loan note whether the loan is commercial or consumer. If it is contained in the note, it is enforceable, even if it is not in the loan agreement.

I have never seen a pre-payment penalty written on a deed or mortgage.