[240racer]

actually if that is the only variable the answer is obvious. Thicker is better for a number of reasons. However, that isn't usually the only variable. First off, before I go any further I want to say that a thinner heat exchanger is more effiecient per weight or whatever.
The reasons that thicker is better, one there is more surface area available for the heat transfer to take place. Also, from the charge airs perspective there is more surface area for it to flow in, which reduces your pressure drop. This is also the reason that it is better to flow i through the 24x5" side rather then the 8x5" side. That is why side to side intercoolers have more pressure drop then top to bottom ones that are the same size. The air has more cross sectional area to flow through and doesn't have to flow as far through the turbulent heat exchanger.
You are wrong when you say the pressure is the same on both sides of the intercooler, in fact the pressure inside the intercooler is quite low. When the velocity is low, the pressure is low, and this is an inverse of cross sectional area. That is why large pipes flow more then small pipes, lower pressure per the same amount of flow. When the air enters the intercooler, it is flowing relatively smoothly, however, the fins in the intercooler and huge increase in cross sectional area make the air lose velocity and pressure quite fast, this causes turbulance. The air must then get back into the little exit hole and when it does this it will not be flowing very smooth as well as being colder, which means it takes up less volume as well, all of these things cause the pressure to be reduced.
Now, with all of the advantages of thick intercoolers and heat exchangers in general that I have given, the reason for thin intercoolers is this. When you increase the thickness from 2.5 to 5" you may only gain a couple percent in effiecency of the intercooler, but you doubled the thickness. It is definatly a case of diminishing returns. You probably would hardly notice a difference in temp drop between the two sizes of intercoolers you mentioned, but I bet you would notice a fair amount of difference in the pressure drop.
Your friends reason for thinner intercoolers and pressure drop doesn't make sense to me, unless he cares about the outside air flowing through the intercooler, which doesn't matter.