I am wondering if it might have been chosen as a joke... 999 is a homonym for the German "nein, nein, nein" (no, no, no), which is rather fitting for a "go away" status code.
More likely they just used it because it's one end of the 3 digit range and a "proper" code would leak information to the unwelcome traffic about what they did to get blocked (making it easier to avoid). Apparently some services already use 000 for other purposes (TIL).
I highly doubt this is the origin. I think its just the last three digit number.