Yes they can use their own license.
Well hold on. If you have multiple customers on one instance of SQL Server, and you want each customer to be able to use their own license, then they will need to purchase the granule to store the license in the database. By default, the NAV license is stored in the Master database, and is shared by all NAV databases on that instance of SQL Server.
If you have a separate instance of SQL Server for each customer, then they would not need to purchase that granule.