We are long time users of both NetSuite and Salesforce. When the two systems were originally configured (before my time), they chose to create a custom record type "client" in Salesforce that is linked to a salesforce account record. The custom client records have 1 to 1 matching customer records in NetSuite. So each custom client record in SFDC has a corresponding NS customer record.

This approach obviously doesn't take advantage of the heirarchy capabilities of both systems. (NS can have nested parent/child customer record heirarchies, and SFDC can do the same with account records)

Seems like the best approach would be to have the 2 systems match, with every SFDC account record having a corresponding NS customer record, with matching parent/child account/customer hierarchies.