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I made my own berd air tube and after installing it I was wondering how much heat is transferred to the brass tube due to its proximity to the hotend. That led me to start wondering if there should be some kind of thermal barrier between the two. Or am I just over thinking this?

I don't think it would make a huge difference to the airflow of the berd-air, but you could insulate the heater block for a better overall performance.
If you have an E3DV6 you can buy their hotend socks or make one yourself as I did.

I've one installed and it works beautifully, check it out: http://www.thingiverse.com/thing:1655134

I have been mulling over whether to get an E3DV6 or stick with my modified stock hot end. I like the idea of using the Ultra copper silicone. I think Ill put a layer or two on the top of the berd air clone.

I never had the chance to use the stock hot end, but i got an aluminum e3dv6 mount from 713 maker and my rostock prints pretty awesome with it. looks good too =)

I don't think it will mater to much if the metal tube gets hot, since you are pushing cool air through it I doubt the air will spend enough time in the tube to get hot...