Hi Chen,
I hope I'm understanding your question correctly.
It seems that you have installed a SQL 2000 Named Instance on a Windows
2003 Cluster. This requires an alias using Named Pipes for setup to run
properly.
Your question appears to be, do you have to remove it?
Technically, no, you don't have to remove the alias. However, cluster, sql
agent, and other local applications will continue to connect to SQL using
Named Pipes. There isn't an issue with this, but if you have an
application that specifically needs to use TCP, you will want to remove the
alias, or at least change it to TCP.
Hope that helps!
Donna Lambert
Microsoft PSS
SQL Server Support