I currently have them removed. Not that it's raining here anytime soon
But I'll be putting them back eventually. I don't like the dismantled engine bay look.
Really the only thing you need for water protection is the RH side front windshield cowling. It keeps water from getting in the cabin air filter and other openings that lead to the inside of the car where the carpet is. I couldn't tell you the effect on the intake temps, but if removing them provides better airflow, then you might see lower temps instead of higher ones.