Dear,
When we are able to scan the MAC addresses from the network interfaces, then we are matching linked assets, based on their MAC. But if the interfaces are not scanned, the diagrams will be indeed flat.
Are you sure the scan is complete, with SNMP? It should show the OID on the asset page to confirm the SNMP scan was successful.
If any doubt you can send screenshots of the scan results to the Lansweeper Support team. They can provide you a better view on what could be missing.