Forum OpenACS Q&A: Re: Forum notifications grouped by subject
Besides "References" the "In-Reply-To" headers is important too. But even using them clients will treat (or ignore) them differently. For example gmail will "create" a new thread if the subject has been edited, even if those headers are present.
Anyhow, about your proposal, forums shouldn't ask acs-mail-lite for a message ID because forums doesn't know the method used to notify the user. The method could be an email message, but could be also a SMS, an alert onscreen, a Voice message, etc. So the way to reference related information would differ.