I have been running Mavericks for about two weeks and I haven't noticed any apps that were deleted during the install.
Some of Apple's apps may be updated during the upgrade, but I'm not aware of anything that gets deleted.
Also keep in mind the App Store will check for system compatibility, so if you can download it to your system without error, then it should install just fine.
However, the only thing that does get deleted is the installer itself once you have finished upgrading. I had some custom folders in the list of favorite before the update and now they are gone.
Whoo I had this issue too, where even after I install XCode4, there was no gcc in my path. I reran the XCode installer and now /usr/bin/gcc is a symlink to /usr/llvm-gcc-4.2/bin/llvm-gcc-4.2 as it should be. See gist.github.com/1096750 for me trying to do that to link to gcc/make for use with OSX brew.
Download and install from the App Store as per my other comment.
However, there's always a slight chance that there will be a problem with the upgrade and that may result in data loss.
There's a 95% chance everything will be okay, but it's always best to be paranoid and back up anything that's critical, just in case.
Your Mac then notifies you when the updates are ready to install.