Paint is a functional part. It provides a barrier between a material that can oxidize (such as steel), and the elements that work to convert it into a non-functional part. Paint has a visual component to it, that may or may not please a particular human eye. Changing the color doesn't effect how the part that was coated functions in the machine.
And engine will jam air borne particulates between piston and cylinder walls scouring both for increased wear. It was determined long ago that the wear increases with the particulates quantity and type found in the air ingested.
Manufacturers can't control where the machine will be operated. So, a device that "conditions" the air to remove engine damaging particulates is included with the machine, so the manufacturer's predictions of engine life can be realized, while reducing warranty claims. They certainly didn't put an expensive air filter on there without darned good reasons of economy, reliability, and longevity.
How many nuts and bolts can you feed the velocity stack on a running engine? Nuts and bolts are particulates too, just bigger.
But, if you only operate a machine with velocity stacks in a "clean room" environment, then you certainly don't "need" an air filter at all.
Given that a filter would be included with the machine, carburetors were adjusted to deliver proper fuel mixtures with their functional parameters and presence included. They are thus tailored to each other. Changing the "looks" of the air filter, also changes the function of the air filter. In this case a "style change" is also a functional engineering change, quite unlike changing the color of the paint on the machine.
It is "simple" to adapt the carb's fuel metering with an air filter change using a dynamometer to load the engine at every operational RPM and read the exhaust gas content on an instrument specific for that task. Then change the carb's internals to correct deviation's from ideal. Then do another machine test on a dyno to verify desired changes. Repeat until the "fuel map" reads as desired.
There are other ways; guess and try with a test track, reading spark plug deposits, tinkering until you get tired of the exercise, or sell the machine to someone else who becomes enamoured with "looks" over proper function.
I understand about the stock airbox may be being the best option, but they are also ugly, big, clumsy to work with, and again don't look good.
Perhaps consider that using the word "ugly" says more about you than the main discussion subject.
I found an urban dictionary defining "ugly". Here are some excerpts for all to enjoy. (I did not just make this up.)

--- A word used by arrogant #$%*s to make them seem like they are the most beautiful person ever and the person that they are calling "ugly" as a lower lifeform.
--- A very harsh word to use, but usually only an opinion anyway. I think someone that calls another person ugly is ugly themselves!
--- A term one would call something when one doesn't see the beauty in things.
"The sunset is so ugly!"
"Only in your perspective.."
In the end, the "best air filter option" is the one that best suits your goals. What were those, again?
Max seat/riding time?
Best photo op?
Be stylish?
Whatever is most popular?
1/4 mile operation?
Ride it anywhere?