What is your version, I found an old note 632096 - ME59N Change of shipping data via BAdI ME_PROCESS_PO_CUST, where modifications by the BAdI were dropped, but it's an old note?
NB: in recent version the BAdi is even used to correct the difference between ME21n and ME59n, see 1758500 - T-code ME59N - PO item numbers are not sequential for an example.
Regards,
Raymond