There's a pretty good debate about this one. I haven't reached a conclusion yet. One school of thought is that the lines are there to use warm coolant to prevent icing of the throttle body. Under certain conditions, the low pressure/low temp. conditions at the throttle body supposedly could cause icing to occur. What doesn't make sense about this to me is that the heat is downstream of the t/b. If you were trying to prevent icing, seems you'd introduce the heat upstream of the icing. Furthermore, it takes several minutes for the coolant to warm up enough to help any - and I'd think the icing potential would be greatest after a cold start.
The other school of though is that the coolant is there to keep the egr spacer/valve from overheating. It does have exhaust flowing through it which is quite a bit warmer than anything around it. The downside of this argument is why didn't the Cobra intakes have it?
Either way, it doesn't seem to make a big difference one way or the other. So do what you like. And if it causes a problem, put it back the way it was. I got rid of the whole egr spacer when I eliminated the egr on mine. So it's a non-issue for me.