Portal is not multi-tenant, and if each NetProfiler represents a customer, then you would want to have a Portal for each customer. But Portal can handle pulling data from multiple data sources of the same type, even in the case of NetProfilers with duplicate IPs....with some caveats.
In the object selection wizard (screenshot below) when building panels in a custom dashboard, you will be presented an option of which NetProfilers you want to include as sources for the data as you build your dashboards/panels, so can 'filter' the panel's objects represented by one or more NetProfilers.
If you use a default dashboard or template that does a “topN” across multiple NetProfilers (i.e. without filtering to a specific NetProfiler), then if the same object (IP address, application, interface, etc.) is found in multiple NetProfilers you would see the object name followed by “(data source instance)” in the panel.
If you search for an object that is found in multiple instances, you would get prompted to select the instance you want to use. Drill-down is relative to the source of the data (the NetProfiler) for the object you drill from.