This library does not really deal with 3D coordinate systems. It is based on JTS and GeoTools and was originally written using versions of those libraries that did not provide good support for 3D. Some early work was done to support 3D, but it is far from complete. Neo4j itself, however, provides complete 3D support for Cartesian points, but not for complex geometries.

However, we did add some support for CQL querying of layers, whether they use WKT or not. This support is wrapped in a concept called Dynamic Layers. This means you define a dynamic layer as a subset of a real layer where the subset is the results of a CQL query. This capability is only available using the Java API, so it is not accessible directly from Cypher unless you write your own procedures.

For an example of some basic CQL used to query imported shapefiles, see https://github.com/neo4j-contrib/spatial/blob/master/src/test/java/org/neo4j/gis/spatial/TestDynamicLayers.java#L76

What is your use case? Perhaps adding a procedure to accomplish what you want is not too hard?