Quoting the mailing-list (which currently seems down):

> Hugo reminds of us of the history of the current logo, which is a reference to the Barcelos Coq from Portugal which Gérard Huet liked, whose shape was drawn by Julien Narboux and adapted/colored for the website by Jean-Marc Notin.

The story seems legit to me, knowing some of the people. I believe there were no jokes in the logo itself, but could be wrong. This was from a time where research projects had many hand-made logos.