I tried with two clean repositories, one bare and one non-bare. Initially the bare one was from stretch (6.20170101-1+deb9u2) and the other from testing (6.20180913-1), the issue sowed up. Then I upgraded the bare one from stretch/backports (6.20180913-1~bpo9+1) aaaand... it worked!
So I guess this is just a backward compatibility issue, would be nice to know if there's any chance to fix it or else I'm going to move my central repo on some other machine on which I can keep git-annex more up to date. thanks m