Intake plenum customizing, what are the pros and cons?

Currently you have an intake that adjusts itself to match the airflow needs of the engine at a given engine load from idle to redline. It allows for a longer or shorter path for airflow through the system based on rpm and engine load to give better cylinder fill in the engine that coupled with the PCM programming gives you a flatter torque curve. That gives you a much better driving experience than what is possible without that tuning ability. When the valves close at lower rpm the intake is through the smaller passages and the airflow speed increases, that increases the cylinder fill of fuel/air mix to give better low-end torque. Now as the rpms rise and the vacuum in the intake lowers the valving opens to allow the larger airflow through the intake to match the cylinder fill rate. That coupled with the VVT system gives a much better torque curve across all RPM ranges. Remove them and the result would be a large power loss across the entire rpm range and would make the vehicle much worse to drive as a result.

Well, I did take all the butterfly valves off at one time just to see what would happen and I did at times feel like there was a slight power loss, but I couldn't notice a fuel efficiency change but thank you for the information. It's not easy to just Google that question and get the answer you just gave me. Because I've tried lol but one more question, please. So, I have a vacuum leak coming from the left exterior side of the rod that runs down inside of the plenum that has all the butterfly valves screwed to them. Could you tell me the correct name of that rod or the bushing things or whatever part that is where it's leaking so I can buy a new one or are they not sold like that so I'll just have to either get a secondhand plenum or buy a brand new one?

Yeah, that is not a typical "hey what is this part" type question. It's doubtful you would see much of a change in fuel use unless you drive around at full throttle all the time as the butterflies adjust at mid to full throttle. The rotary valve opens at lower levels. There are bushing kits for those manifolds available online such as these:

https://www.amazon.com/Klifex-manifold-Hyundai-2921037280-292103E055/dp/B0B6Q36YH9

How well they work, I don't know, the last one I did got a replacement intake because nothing else existed. I would look at those and see if anyone on the Santa Fe forums have used them.