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Lotus Notes database encryption is actually a database property that can be set using the create replica dialog. It also can be set or cleared later in the "Encryption Settings" dialog, found in the "Basics" tab of the database properties dialog.
Unfortunately, I've found that the encryption setting isn't exposed programmatically, although I haven't investigated DXL or the database design class available on the LDD sandbox for references. Nonetheless, you may not need to set it. Starting in Lotus Notes Domino R6, local replica copies receive medium-level encryption settings by default. If this suits your needs, you can create the replica:
Dim Session s = new NotesSession
Dim replicaCopy as NotesDatabase
Set replicaCopy =
s.currentDatabase.CreateReplica("","filename.nsf")
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