Just an update on this - I am still having the same issue. But, oddly, I have noticed that if I copy and past the link (the one I've created in OneNote) into Word then I can click it and it opens the file.
Therefore the link is working fine, and pointing to the correct file on the network. But it does not work in OneNote.
Also just to be clear - all the links were working fine in OneNote until I upgraded to Office 365.