The two coolant lines supplement the emission controls; they "pre-heat" the throttle body chamber when the engine is up to temperature. The reason was, heating the inlet air will keep hydrocarbons stable in closed-loop. In practice, though, I'm not sure if they really make a difference. Most GN owners have capped the pre-heat lines off. This was a popular thing to do back when the 160 degree thermostat mod was started.
The engine runs the same with or without that change as far as I can tell.