If you need a tool that will lock down USB ports and eliminate sneaky auto-run malware off your flash drive, secure usb Suite is worth a look.
Assuming that they are carrying some kind of malware before you even put them in your USB port is smart. However, without the right tool to protect your system and home network, you could wind up with a huge problem. While this app does secure usb use TSR-styled technology, it shouldn’t cause any kind of performance based hit, though its monitoring of USB based traffic and disk activity may at some point interfere with USB communications. Regardless, this is a must have app.
The simplest guard is an embedded board with PIO, connections to the computers, and running a microkernel OS with carefully written drivers. OpenBSD on a more powerful embedded board or even old school server with certain Open Firmware changes can do as well. Worst case scenario, a regular computer with open BIOS and Linux with assurance enhancing extensions (eg SVA-OS, SMACK). Remove usb security any piece of code from the system you don’t need. If it has to be there to compile, just change the code to return successfully instead of doing something. 😉 Just make sure that the application level of it uses no dynamic memory allocation, gets size/hash before hand, consistently checks timing to know if device is stalling on transfer, and does bounds checks on arrays/buffers.