Well the node name is your hostname as recieved from your devices so if your talking about renaming the nodes why dont you change the hostnames but i fail to see why you would rename your naming convention in the first place. LEM'S primary functionality is to analyse syslog and events from nodes, not node management so the management config is based on the alerts for the syslog and event traffic, hence the grouping and organisation of alerts, not nodes. LEM' is not a node management tool.
The node names in LEM and NPM should be exactly the same as they are pulled from the devices. No there is no LEM NPM integration which is a shame. To achived the same interfaces on LEM as on NPM, list resources in NPM and make sure that the interface is selected that syslog is reporting.
As for your implementation, if the hostname is not appearing on the devices on LEM, presuming you are talking about layer 2\3 stuff, then i would double check snmpconfig again. In all them LEM installs i have worked on, i have never seen a case where hostnames were not retrieved. I would also go over and see if all LEM ports are being allowed. I would also check if the ports on LEM appliance are unrestricted as per the documentation. If it is servers with the issue i would also check if the agents are currectly deployed.