It would definitely cut down in efficiency. I don't have two cars of the same set up to provide any accurate data. ZZP, over the course of a lot of remote tuning, was impressed by my lower IATs in my supercharged car with a dual pass plate and NACA ducts (no fan) installed. A lot of WOT pulls on 95F degree days.
A fan install may produce better results, with a no cutout splitter, providing some form of constant air movement. When the splitter is installed you're definitely trapping more heat from the radiator, which will heat soak that intercooler more quickly, in the front of the car. Nice...on those cold mornings...but not ideal for cooling. High rear, or side mount, intercoolers would probably be a better option for cooling if you're sealing off the bottom of the car.