The reason that happened is When you run Windows 2000 setup, if another Windows 2000 installation exists on the partition you just installed Windows 2000 to, even if you used a different folder, setup creates the All Users.Winnt and Default User.Winnt profiles. This may happen if you tried to overwrite your existing Windows 2000 installation because of the difference is SIDs.

You can delete the unused ones. But I would make sure that I delete the correct ones. You can see what All Users and Default User profiles are being used by the Windows 2000 instance you just booted, inspect the data values of the AllUsersProfile and DefaultUserProfile Value Names at:

HKEY_LOCAL_MACHINE\Software\Microsoft\Windows NT\CurrentVersion\ProfileList.