The /Encrypt dictionary will never be encrypted. It is the key content of a PDF document that contains information how to decrypt data strings and streams. If the /Encrypt dictionary is not present (or inaccessible in some manner), it either means the PDF is not encrypted or the PDF is encrypted but corrupted.
PDFNet offers low-level SDF API which allows you to work with any aspect of a PDF document. You can use the SDF API to encrypt PDF documents with Public-Key Security Handlers.
We value your feedback and we are always improving PDFNet SDK. An API specific to Public-Key Security Handlers will be considered for future releases of PDFNet.