As it is well known that QKD systems are prone to simple MITM attacks… what authentication techniques are being used in QKD to prevent those attacks in practice?
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The standard answer in the research literature is to use information-theoretically secure message authentication codes, typically universal hashing (aka Carter-Wegman authenticators). Of course, you could use computationally-secure message authentication codes, like CMAC or HMAC, if you wanted, though that would partly defeat one of the reasons for using QKD.
That said, in practice QKD is a bit silly. QKD solves a problem that most people don't have, so it is basically a fancy useless toy (albeit a very expensive one). If you're considering using QKD in some practical deployment, my advice is: skip the QKD, and just use a TLS or IPSec VPN. There, I saved you $50,000; don't spend it all in one place!