This is an installation program issue, NOT a Windows 2000 issue.
NOTE: Older versions of InstallShield exhibit this behavior.
To clean up after an uninstall that leaves a folder behind, simply use Explorer to delete it.
To remove any orphaned icons, right-click the Start button and choose Explore. Navigate the Start Menu folder and subfolders untill you find the shortcut. Delete it.
If you didn't find it, right-click the Start button and choose Explore All Users.
NOTE: In the case of older versions of InstallShield, the problem is that the uninstall doesn't use the same CSIDL value to uninstall, as it did to install. Other versions of Windows didn't care, but Windows 2000 does. Do NOT try to resolve this problem by installing a new version of the installation program, you will cause real damage, as apposed to the minor annoyance you currently experience.