Like any proper Windows program, things in %APPDATA% are not supposed to exists after a clean installation. That folder is supposed to contain only YOUR personal settings after using a program.
So, in case of GSX, the %APPDATA%\Virtuali folder will be created for the first time only after you change a default setting, create a new airplane configuration, customize an airport, create a custom logo texture, etc.
If you had it full of your own customizations, and now it's not there anymore, I'm afraid nothing other than restoring from backup ( maybe the files are still in the Windows Recycle Bin ? ) can restore such files, since they are not coming with GSX, they were created by your own usage.