Hi Blocker, its not a stupid question,
Yes you need to allow for the 4" pipe,
I too would like to do a vertical with a led, but at the moment they are way too expensive, I am not sure at the moment how good the led's but I suspect they are no where near as good as a hps light at the moment.
I would save your money until you see a really good grow using led's by a respected member of one of the grow forums, as manufacturers and vendors tend to exaggerate what their products will do.
good luck
Heath