I actually remember using message IDs to reference other postings. Newsreaders had commands to jump to a certain message ID. You had to copy the message ID from the posting, but on Unix that was just a double-click, and a middle-click to paste, so quickly accomplished.
At some point a thrrad becomes irrelevant because of parallel discussions in other threads, being able to easily redirect to a specific point in another thread helps a lot. But that requires an URL, and messages ids weren't used for that purpose.