It looks like they removed the sound file from UIKarmaUp and UIKarmaDown, and if you add "Karma" to the filter on Game Settings in the GECK you can see they modified a variety of settings that affect karma. The ones I am guessing in charge of notifying the Player of karma loss or gain via message are the following:
- sKarmaMajorGained
- sKarmaMajorLost
- sKarmaMinorGained
- sKarmaMinorLost
One way I believe you can change them back is to make a plugin that attaches the modified flag to those sound files and game settings and load that plugin lower in your load order then the FO3 Wanderer's Edition - Main File.esp.
Another way is to just modify that FWE plugin directly.