Having had a s2 exige s260 and doing allot of research I hope this helps you..
First off it's not the supercharger that overheats, its the induction air that gets hot causing what's referred to as heat soak. Elise's don't have a intercooler and run a smaller supercharger the mp45 unit which is capable of 220bhp.
In the s2 exige the unit is a mp62 fitted with a intercooler mounted over the engine itself, which isn't ideal. The more it's pushed obviously the hotter the engine gets, heating the metal intercooler itself.
Several very in depth tests show that the roof scoop system, small and large scoops do assist in the cooling, the larger option only over around 110 iirc. The smaller scoop was actually more affective upto that is better as its not taking the hot air from the radiator straight off the windscreen into the scoop.
The biggest issue is the scoops feed directly into a letter box which is very constricted, hence why if you stay the intercooler route, the bigger proalloy unit with side scoop additional feeds.
The best all round is to go charge cooled and negate all the above issues.
Back to the elise front... Also bear in mind that the s2 sc and s3 sc are 2 different engines... You either get the s2 with the rev happy 2zzge or the newer 2zrge which dosnt have the high rpm scream which I loved on second cam. IIRC the higher powered s3 variants also run a charge cooler system but I may be completely wrong on that.
Another Option is to find a very rare S3 RGB Elise, which had the very last of the 2zz engine in an s3 body.