This video explains the TWO distinct ways that NX uses Reference Sets:
One, to control display of component geometry at higher levels in assemblies, and Two, to identify geometry to be considered for component mass properties.
It's important to note that the settings for these two usages are distinct... Changing the display of a component (show/hide or display reference set change) does not affect the mass properties calculated in the assembly. This video shows that you can choose which reference set is used for mass properties calculations, but that this setting is independent of the use of Reference Sets for display. I hope this is useful for you!