K-9 Mail only supports setting a handful of header fields from a mailto: URI. In-Reply-To is currently not among them. But I see no harm in adding support for it.
If you want to submit a patch have a look at MessageCompose.initializeFromMailto(). You’ll also have to modify the MailTo class to add support for In-Reply-To.
K-9 Mail will properly set In-Reply-To and References when replying to a message from inside the app.
Thanks for the quick reply. As soon as my hands touch a keyboard in my free time I’ll send a patch for the in-reply-to (and subject if not already covered).