As far as I know, FM will accept input from a bar code scanner as it accepts input from any other device, such as a keyboard.
Most bar code scanners work in "keyboard emulation mode". You hook them up, scan the bar code and the text appears at the location of your cursor just as though you had a very fast typist typing in the data. You can usually program a scanner to put characters at the beggining and end of the scan you can use these with KeyStroke script triggers to control FileMaker's response to the scanned input.
There are several threads here in the forum on this subject you can pull up with the search tool for more research on the subject.