Not good to know. I just migrate from version 3 to version 4.
I had a lot of servers/databases flags for ignore. It's specially important while connecting to SAP databases (about 87,000 tables/views). On my initial tests, query analyzer consumed about 800MB of ram.
Let's see how it will work after some days connecting/disconnecting from a farm os servers.
My vote to recover this feature for version 5.