Yes, as I noted in my "further thoughts" follow-up, by the time your code accesses the document, the Notes back-end APIs will have already decrypted the message, so $Seal will no longer exist in the in-memory note. So that technique is really only useful when running in an agent on the server -- because the private key to decrypt the email isn't available, therefore the APIs can't decrypt the message. If a server agent is your real goal, I assure you that the technique will work. You just can't see it work in the debugger.
But if you are writing client-side code that runs against the user's own mailbox, then the automatic decryption done by the APIs is your enemy. The best you can do is check doc.hasItem("Encrypt") & doc.Encrypt="1", but in my experience it is not 100% reliable.