Windows 2000 supports deep shares, the ability to map a drive letter to a folder below a share.
Windows 2000 maps the %HOMEDRIVE% environment variable to a users home folder, even if it is a few levels below a share.
If your home folder is at \\ServerName\ShareName\Folder1\Folder2\%UserName%, the %HOMEDRIVE% variable is set to \\ServerName\ShareName\Folder1\Folder2\%UserName% and the %HOMEPATH% variable is set to \.
If you wish to retain the Windows NT 4.0 home folder functionality, use Group Policy to navigate to User Configuration / Administrative Templates / System / Logon\Logoff. Double-click Connect home directory to the root of the share and Enable this GPO. This will cause the %HOMEDRIVE% environment variable to map to the share (\\ServerName\ShareName), and the %HOMEPATH% variable to resolve to Folder1\Folder2\%UserName%.
NOTE: If you have a Windows 2000 server in an NT 4.0 domain, use Start / Run / Gpedit.msc / OK to set this GPO.