When running a query on a feature class which has primary and secondary geometries, only the primary geometry is added to the legend by default.
If the Legend>Add Query command is used to add the query to the legend, both geometries are added.
Why would adding a feature class to the legend operate differently from adding an attribute query?
There are a couple of answers here:
By the default only the primary geometry is returned since it was the only geometry field used in the query. Example: if a user finds all points within distance of 10 meters then only the points are returned although they may have secondary geom's that did not meet the 10 m criteria.
Returning only the primary is the standard for other queries. Certain Functional Attribute queries return geometry such as the FILTERHOLES function. This function returns the holes of polygons as the primary geometry and adds them to the legend, although the secondary geometry the outside part of the polygon is not automatically added to the legend. Adding this automatically would make the filtered holes look like they weren't filtered at all.