Use of desktop shortcuts in lg. cos.

Is using desktop shotcuts, with today’s technology, still a big issue in large organizations? Some organizations mandate using (in a Novell environment) NAL or similar applications to control launching of applications. Winstalls work great but in the end they point to a permanent network location.
End Users prefer to have desktop shortcuts to their apps. There is the old argument that they are harder to maintain (e.g. app moved to different drive etc.). A few comments on how your large organization handles this would be very helpful.