There is no native functionality for encrypting a PDF document from within BusinessObjects Enterprise. Additionally, none of the BOE SDKs are able to encrypt a PDF document either. Generally speaking, if it is not possible in the product (BOE) it's not possible with the various SDKs.
I am not aware of any third party tools that can do this from inside BOE either. If you haven't done so already you may want to post a question to the [Business Objects Board|http://www.forumtopics.com/busobj/index.php?sid=1037068e7b26619422be6a7b18a8c2ee] (BOB) to see if anyone there has a suggestion.