It can be useful, for example, to neglect the mass of a supported surface that participates to a large amount in the structure of the total mass, but does not have a major influence in the dynamic response of the structure. When this kind of mass is considered, it can be difficult to reach effective modal mass factors of 90%. This example is detailed in the image.
When masses of elements are neglected, the whole dynamic analysis changes. Equivalent loads are not generated on these points, for example. Also, the results of the time history analysis are determined with a changed mass matrix.