Amrsitice doesn't appear to affect some pirate units and rebel units (tec insurgency upgrade). I tried to defend a teammates homeplanet under attack from an extreme pirate raid and armisitice didn't stop the seige units from firing. This also happens with rebels created from the tec insurgency.
I can't wait for the day where the trade and refinery ships start moving instead of taking a loooong coffee break for the whole game.