The old single-track tunnel is no longer used by the railway, though it is still used to route a pipeline under the hills to Kowloon.
If you zoom in on the satellite map above, you can see the disused cutting that leads to the old portal. It's a short distance east of the current tunnel portal.
Thanks to Peter Crush for this photo of the portal taken during its construction: http://i1103.photobucket.com/albums/g468/chinarail1/Beacon-Hill-Tunnel-ShaTin-FER-Nov1909.jpg
You can trace the route of the old tunnel on the government's mapping website: http://www2.map.gov.hk/gih3/view/index.jsp (It isn't shown by default - click the "Detailed Map" button, and zoom in to levels 6 or 7 to show it.)