You can no longer disable Named Pipes on SQL clusters as of SQL SP3. MS PSS has acknowledged this change although they have yet to document it anywhere.
The reasons given for this change:
1) If other protocols failed, they wanted at least one protocol to be available. For example if TCP/IP is enabled yet SQL Server fails to bind on 1433, Named Pipes should still be able to respond.
2) Prior to SQL SP3, if you disabled Named Pipes and re-enabled it you would an encounter an issue where the local machine name would be populated rather than the virtual server name. For example: \\.\pipe\$$\local machine name\sql\query instead of \\.\pipe\$$\virtual server name\sql\query