Hi Xavier,
There is no security concern with either merging or not merging the documents because the data is always stored securely in DocuSign’s servers.
A customer may not want to merge documents for a couple of reasons. If users are using Digital Signatures (a typical practice outside the US), additional cryptographic information is added to the document. This additional cryptographic information is invalidated if any change is made to the PDF (such as merging the certificate of completion). If a user wishes to keep the cryptographic information associated with their Digital Signatures, they would not want to combine PDFs.
Otherwise, a user may simply wish only to see the original PDF that was signed without the CoC.