Accurate estimates and forecasts of mesoscale eddies in boundary current regions such as East Australian Current (EAC) are important for understanding weather and climate. The EAC jet and eddies have also been shown to be central to influencing marine heat waves, cross-shelf exchange, biological abundance and connectivity. However, the dynamic nature of eddies requires data assimilation to produce accurate eddy timings and locations in ocean model simulations. While data assimilating models produce skillful representation of surface dynamics, simulated ocean states are rarely assessed below the surface, due to a paucity of observations. Hence it is not clear how data assimilation impacts the subsurface eddy structure. Here, we use a suite of Observing System Simulation Experiments to show how the subsurface representation of eddies is changed within data assimilating simulations when assimilating near and distant observations. We also examine the representation of ocean heat content, an important quantity for understanding marine heat wave events. Two possible manifestations by which the data assimilation process impacts 3-dimensional eddy structure are presented. Our analyses demonstrate the need for further basic research in ocean data assimilation methodologies to improve representation of subsurface ocean structure, particularly in western boundary currents such as the East Australian Current.