Within the book itself the clacks system has its own technical protocol which is briefly touched upon. The "overhead" is essentially packet or request metadata.

From the LSpace wiki, GNU is a metadata that means:

    G: Send the message onto the next Clacks Tower.
    N: Do not log the message.
    U: At the end of the line, return the message.

And yes, it is almost certainly a reference to GNU as in "GNU's Not Unix". =)

https://wiki.lspace.org/GNU_Terry_Pratchett

Quite intentional.

It's Terry Pratchett, so of course it's an intentional reference.