"Encrypted" setting not remembered after editing saved draft
The setting that a mail should be encrypted gets lost in the process of saving the message as draft and editing it again. To reproduce: Write an e-mail, set it to encrypted, then save it to the drafts.
In the drafts it is marked as encrypted. When you edit it, this is the time the setting is changed from "encrypted" to "unencrypted" without user interaction. If you do not remember to set it to encrypted again, the message will go out unencrypted.
Related to the issue about signature. We currently have no way of persisting state about drafts, but there was talk about supporting arbitrary properties on messages in notmuch. Might be a solution. In this particular case the 'encrypted' tag might actually be used aswell.