In this answer I posted a few links that I formatted using backtics. Because of the new background color and the way the links are formatted it isn't clear right away that they are clickable. (It just looks like they are being syntax highlighted the same way code blocks are.)
As pointed out by rcartaino, hovering over the link does not show an underline like regular links. The only visual clue a user is given that it's a link is the cursor.
I would recommend that links formatted as code should be underlined.
(These results come from Firefox 3.5, and Chrome 3. Underline works in Opera and IE 7)