The differences with an exposed air intake open to the hood temps and the types that pull cold air from inside the fender are subtle. One involves the fact that the inner fender area is a "high pressure" zone for our cars - you get a slight ram air effect there, similar to what is seen from cowl induction in some cars.
The cooler temps from pulling the air from the fender vs under the hood have more to do with slightly improving gas mileage in hot, stop and go conditions than any big gains in power output.
Just as with any of these types of mods, there are some advantages to be had from removing restrictions WHEN the engine is being affected by the restrictions - ie, the gains will be modest-to-zero if your particular setup is not being compromised by the reduced flow. This rule of thumb pertains to many modifications, including exhaust components and running larger TBs, MAF's, fuel injectors and so forth. If the engine does not NEED additional flow, supplying it will gain little, and may even hurt performance if subtle tuning issues are not addressed.
I know this is complicated, but the short answer is that well-designed CAI systems WILL give modest gains which are VERY similar to those to be had by upgrading the air filter - removing the silencer - and replacing the crennelated plastic intake hose with something with smoother walls.
One comment: If a positive displacement supercharger is planned in the future, RETAIN your old parts whichever way you go - most of them use the OE air box and so forth as part of their parts list.