A lot of the guy's who run in the desert have moved back to regular old paper element filters. The K&N's seem to allow a lot of fine particle dust to get past them.
But I'm guessing you're talked about CAI (Cold Air Intake).
I forget if you have a YJ or TJ, but since you mentioned the hour clagg thingy, I suspect it's a YJ. What the majority doesn't understand is how iar moved and travels. Instead they just remove everything in it's path, thinking that bigger is better.
Most people call it a restriction. In basic terms it is. What is it is a venturi. Like in a carburator. The bottle neck speeds up the air but narrowing the passage slightly. This causes a vacuum which is designed to pull fumes from the CCV.
I don't believe the air flow is really reduced significantly. At the venturi the air speeds up so there should be about the same CFM. This is why engine vacuum is reduced. To create a vacuum, air needs to be moving at a high speeds. This is why many CAI's throw off the MAP and cause a lean senario. Since brakes run off vacuum, they are also reduced. Many people think their bad brakes are because they changed the tires or added lift, but really, engine vacuum, comes into play here.
The other thing that people don't really tank into account is teh pulse wave. As air moves down the tube, it creates a pulse wave. The pulse wave travels up and down the intake. You can tune the pulse wave with intake length. Optimal timing would have the pulse wave arrive at the intake valves as they open for the intake stroke. This would help get more air into the engine with every cycle.
You mentioned heat. This is the main difference between the cheap and the expensive CAI's. Cheap ones slap on a filter at the end of the stock air tube or on a short tube with little consideration in routing. Results should be poor. You're not only changing the length and pressure of the air intake but you're also allowing a lot of engine heat into the intake. Hotter air is less dense and less dense means less air and that means less power.
This is one of the reasons I switched from a CAI back to the stock air box. I even use a paper element Fram filter. What differences did I see? Well, first off I noticed more engine torque on the low end and the brakes firmed up a bit more. Btw, I still have the venturi and the turndown at the front of the airbox on.
Now if I was going to change the setup in any way, I'd be more inclined to keep the stock airbox and use a tube to route the front intake to a better location. Perhaps to the front of the radiator. This would help increase air flow without any of the side effects. Although, I haven't had time to test this.