My shop currently uses Windows 7 Pro (on desktop PCs). I consider to upgrade our clients to Windows 8 (or 8.1). I've just been told that if I upgrade, all the software installed on them will go away. Is this the case, and if so, is there a way to avoid re-installing all applications?
Perhaps the person you were talking to was confused and thought you meant to reimage them with a new OS, instead of upgrading. You can certainly upgrade them and it works much the same way as every previous upgrade has - lots of things move around; on rare occasions stuff breaks, but generally the process is pretty seamless and you're in the new OS.
That said, in an enterprise environment usually this is to be avoided, and instead the thing to do is to build a new computer with the new OS and the user's preferred applications (using your deployment tool), and use the USMT (user state migration tool) to move over settings. The upgrade process, if I recall, uses some of the USMT functionality internally, for what it's worth.
The reason for this preference is that it minimizes downtime, allows rollback (if you're into backing out of changes), and minimizes risk in the event that the upgrade doesn't go as planned (renders the system unbootable or some other infrequent error).