It depends on two things. How you drive it and how the engine/transmission itself responds to the modifications.
If you want more power to go faster, then of course you're going to loss economy. Its hard to get around basic physics and chemistry.
I am not familiar with your drive train either. If you have 5th or 6th gear, you most likely won't see any highway gains, and have the possibility of losing MPG. Pulling more air through the system will increase full consumption as the engine management attempts to maintained program A/F ratio. If you have a 4 speed where you encounter flat spots of acceleration, opening up the intake and exhaust will help you maintain less throttle to obtain higher speeds.
Its a trade off, you'll have to try for yourself. You could always ask the people with Kia Souls if anyone has noticed a difference in fuel economy with those modifications. You'll need to find an honest opinion from someone who accurately tracks their mileage. Most of the time, if you putting on intakes and exhaust you're not worried about FE and new accessories "encourages" you to drive faster and will lose FE. You need to find a driver who kept their driving habits the same given a new intake and exhaust to get an accurate answer.
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