How does disabling a network protocol affect SQL server performance
Yes, IMHO you should disable named pipes and use only TCP/IP for better performance. You can force this in the connection strings for your apps and change them one at a time, rather than just shutting off named pipes and then getting a bunch of complaints:

Data Source = tcp:IP-or-host-name[\instance-name]


Don't shut off named pipes until all your apps are using TCP/IP. You can check what your apps are using via sys.dm_exec_connections.net_transport - this will have values such as TCP or Shared Memory. You can check the program too via a query like this:

SELECT c.net_transport, s.program_name, c.client_net_address
  FROM sys.dm_exec_sessions AS s
  INNER JOIN sys.dm_exec_connections AS c
  ON s.session_id = c.session_id;




However, for your second question, using one login or multiple logins won't affect performance much unless you're at the upper end and exceeding your pooled connections limit. In most cases consolidating into a single login will just make it much harder to later audit etc.