In a nutshell.....cartoon version....The inner cowls serve a purpose of DIRECTING air into the radiator, so the cooling system works as designed.
By removing, or cutting these pieces up, you are no longer directing air into the radiator, and you'll find the front wheel/fender does a great job of blocking, and restricting air flow into the radiator etc.
The air then is directed straight back into this dead air space, which ends up getting heated up by the engine, which in turn heats up the side of the gas tank and frame etc.
It turns the entire area into a giant heat sink.
There are MANY different things that cause heat on these bikes, and several of them are easily fixed, without damaging stuff etc.
Just some of the things could be as simple as spark plug type and heat range, what type of seat you have on the bike, and what position is it in?
What size the rider is, and does the riders clamp down on the tank with his thighs?
Have the pair valve reeds been cleaned? are they no longer allowing air to re-circulate and cool things down?
Does the bike have an aftermarket exhaust? A K&N filter causing it to run lean?
What altitude is it operated at? What type or grade of fuel is used?
What type of oil is used?
What type of coolant, and is the T-stat frozen open?
How long does it take to reach the first bar on the temp gauge?
To date, there has only been TWO ST's that I have not been able "fix" to the owners satisfaction, and ONE of these turned out to be caused by Thyroid medication, and once his meds were changed, the heat was no longer a problem, and the SECOND one was because the rider was very short, and over weight, and kept the seat in the lowest position, and forced his riding position to straddle the tank and reduce air flow around his body.
His bike was ridden by two other riders (myself included) and heat readings were done, and his bike was no hotter than the other two bikes, and he complained that the other two bikes (mine included) were just as hot etc.
If you want to reach out and talk to me on the white courtesy phone, I'd be glad to try and help you figure out how to correctly tune your bike.
I have removed MANY inner cowls that had pieces cut out of them, cut into frames, holes drilled in them, and replaced missing cowls, and I was able to reduce the heat in all these bikes.