We have recently stopped including the point spatial data with our monthly GIS data package. The primary reason for this change is that the point data are often misinterpreted as representing actual element locations or observations. In fact, the point layer simply represents the centroids of the Element Occurrence (EO) polygons, and is intended to only be used when displaying CNDDB data on small-scale maps (i.e., maps that are zoomed out to show large areas). Furthermore, the polygons we create are not actually point observations, but instead reflect summary records for a given species (element) at a given location, and the size/shape of the polygons are based on the uncertainty of the location information associated with the records being summarized. This methodology has been employed by natural heritage programs for several decades, and the CNDDB bases our mapping standards on this Element Occurrence model in order to stay consistent with what other programs in the NatureServe network are doing (in other words, we want to make sure that an EO in California represents the same thing as an EO elsewhere).
If anyone is interested in learning more, you can read about the Element Occurrence standard on NatureServe's Element Occurrence Data Standard web page. We have created a document that provides additional information, and includes instructions on how to generate a point shapefile using the CNDDB polygon layer if you have a need to do so: Creating Point Features from the CNDDB Spatial Data (PDF).