Oh, funny, I'm working on something similar for a course at school, too: an IP over Avian Carrier modem. (I convinced some folks to build one with me :b). In our case we print the barcodes with a thermal printer, so there's an interesting constraint that we need really simple, easy to scan barcodes that fit on that paper but are still data rich. I have happily ignored the printing / scanning part of the project, but I think we're sticking with Data Matrix, and I've set an MTU of 300 bytes on our network interface just to be sure. We're using tun/tap, too! It's really handy.

Alas, carrier pigeons are difficult to employ, but that's okay. Part of our goal is to demonstrate network protocols in a tactile way, since you see every frame that gets sent and received as it happens. (And read them, too - we're including a hex dump with strings). I think it's a fun alternative use for projects like mine and like the article's :)

Haven't thought about performance much at all, so I'm curious to see what the author has in mind there.