One way to hide an application from Add/Remove programs is by settings a SystemComponent registry key for the application in the Uninstall path.
For 32-bit applications, the Uninstall path can be found at:
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\Microsoft\Windows\CurrentVersion\Uninstall
For 64-bit applications, the Uninstall path can be found at:
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall
Inside the Uninstall path, find the application you want to hide. Once selected, add a new DWORD 32bit named SystemComponent and set the value to 1.