The short answer is yes - in both older & newer versions of HyperLynx we account for planes. We significantly improved the simulator in 9.0 - you may want to check these:
I'll try to summarize - in 8.2.1 and earlier, the simulator assumed plane layers were continuous, uniform, and infinite (i.e. no gaps, splits, edges). Therefore, it did not account for edge effects when a signal travels parallel with the edge of a plane on an adjacent plane layer. It did not account for coupling between a trace and an area fill on a signal layer. And it could not account for disruptions in the return current when a trace crosses splits in a plane layer. You could use RMB > Field Solver Output to look at which conductors the simulator was accounting for.
In 9.0, the simulator accounts for plane edges. It can also account for coupling between a trace and an area fill (Setup > Coupling Thresholds > Include trace to area coupling). It also partially accounts for traces crossing a plane split - it still cannot account for disruptions in the return current (you need HL 3D for this), but it will account for the impedance discontinuity within the trace. Field Solver Output will also show you the referenced conductors - you can view the area fills and plane gaps.