I guessed that you had an induction kit fitted, this would have been a good safe option if you had fitted the kit yourself and still had the standard filterbox etc, not sure of the truth behind this but I have seen alot of threads/feedback stating that the bonnet scoops can upset the airflow into the intake by causing a massive turbulence within the engine bay at speed which in turn could upset MAF readings and engine performance (I have not seen any proof of this but I do know that the straighter the airflow is presented to the MAF the better it works and the faster the air will flow though the system), so I would recommend that out of the two options you have to fit the filter in the wing as high up as you can, I have also seen these recently Bypass filter link, the thought behind this piece of kit is to prevent/reduce the risk of ingestion of water through wing mounted filter setup, it sould be mounted as high up the intake system as possible (can explain further if required ).
Hope this helps
Cheers Iain