Well, I think you should know what Full/Normal Uninstall does, when you have this option in HC (http://www.microsoft.com/technet/prodtechnol/sppt/sharepnt/proddocs/admindoc/owsd02.mspx)
(Normal)uninstall just disables FP extensions for web site, while Full uninstall disables extensions, deletes system folders created by FPSE, deletes related groups and users (Windows Local Users and Groups)and Registry entries created when you enable FPSE for that site.
So, if you do not want to leave all kind of garbage you should use Full Uninstall. In HC there is an option for Full uninstall, but it does not work! HC just disables FPSE and leave all other things on server.
I do not know how exactly HC uninstalls FPSE, but I suppose that you use owsadm.exe tool, and that you should change switch when you call it. Proper command for Full uninstall should be something like this:
owsadm.exe -o fulluninstall -m test.com
(This is how it works with FPSE2002 on Windows 2003, but I think it works same way on Windows 2000)