The 'malicious file system' on a USB stick is not something to worry about - the firmware of your USB stick is. People (ie for-fun hackers) modified firmwares o

The 'malicious file system' on a USB stick is not something to worry about - the firmware of your USB stick is. People (ie for-fun hackers) modified firmwares on USB sticks to make them look like HID keyboards and send commands to target computers - it is well enough in the capabilities of a determined adversary to own your internet machine and implant something on your USB stick. For secure airgapped computers I'd use one way low tech comm channels with no side bands, maybe IR or sound? (if you trust the device drivers)