Try connecting 2 USB barcode scanners first and checking to see if what you are afraid of has happened. I suspect that all barcode digits are sent in one packet, while interrupts from other keyboard devices are on hold - so you will not get two barcodes "interlaced" together.
It is impossible to have more than one stdin, not literally. Other options depend on the OS you are on - on linux, perhaps the drivers provide you with different character devices for different scanners. On Windows, I believe that you will need to learn to speak the USB HID protocol ... best if you don't need to do anything.
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