waiting for barcode scanner output, while main program continues to run

[DeaD_EyE]

I haven't run the code. If you do not need access to thread and q from other functions, you can creates them inside a function.
I think your problem comes from scanner_thread.join() inside the loop. This blocks your code until the thread ends, but the thread does never end.

import threading
import serial
import queue


def thread_scanner(q):
    # serial.Serial should support context managers
    with serial.Serial("/dev/ttyACM0", 9600) as ser:
        while True:
            barcode = ser.readline()
            q.put(barcode)


def mainloop():
    """
    Starts the mainloop to print barcodes
    
    Everything else must be done inside this function or
    you put it on module level, if it's required.
    """
    q = queue.Queue()
    scanner_thread = threading.Thread(target=thread_scanner, args=(q,))
    scanner_thread.start()
    while True:
        barcode = q.get() # get blocks until it has an element available
        q.task_done()
        print(barcode)


if __name__ == "__main__":
    mainloop()

Since Python 3 serial.read* return bytes. You can decode them, if it's ASCII or some other kind of encoding.
If it's binary data, you've to convert it into data you can work with.