Hi,
I see your point for WhoIS, but NSLookup and Traceroute tools use your configured DNS Server on the LEM Manager. I have validated this on my own installation, by querying several devices on my local domain and domain names external to my organisation and they return the expected results. Can you confirm that you have your LEM manager configured to use the correct DNS servers (i.e. a local DNS server with a forward lookup zone in your network).
Here is a Traceroute to bbc.co.uk
External NSLookup
Lookup to a sever on my training LAN
Traceroute to a server on my Training LAN