Use of QR codes in academic publications
I think this is a matter of convention and necessity.  As you already point out, most documents are online.  If something is online or in pdf form, having a QR code that is scanned with a phone is a waste of space, as the user can just click on the link instead.

In the case you are describing, I find it rare that any document would be only available in paper form, if it was made at any time since the invention of the QR codes existence (which it would need to be in order to have one).  

The question also seems to be a rare situation.  You are saying a new document is published, but it is only available in paper, but it contains other information that needs to be seen online.  It is hard to imagine a document which is in paper, that contains some valuable data that needs to be viewed on an electronic system, in which the time saved from scanning a QR code on a phone and dealing with a phone screen outweighs the use of a tiny url or permalink typed into a computer.