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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