Throw some silicone joystick protector rings on your sticks if you haven’t. Makes the joystick almost completely silent even when I slam them against the shell, and as long as they’re seated right and clean they’ll still slide smoothly against the shell. Just make sure to run through the calibration script so you still have full joystick range after adding them
Either that, or they use specific tools that they can’t or won’t replace and which don’t work on Linux. Usually it’s creative or engineering software. There are usually good, Linux compatible, open source alternatives, but they’re not the same as industry standard tools that they need to know how to use and be 100% compatible with. Windows or MacOS is your only safe bet there.
If you’re a mere hobbyist and interested in learning new tools it’s an entirely different answer. You can try out the windows versions of the alternative software first, then try switching to Linux down the line when see the greener grass.