I think they may repeat them again, but that may prove difficult as the amount of people that play the single player is likely decreasing. Ubisoft might change something - I think I recall Mr Shade saying they might change plans in the future, but don't hold him accountable for it.
The challenges did repeat a few times -but I will check if they are finished for now, and/or if they have any plans to release the content for those people who didn't have the game at the time
Yeah I missed all the events except the "last" one. But I don't change my sails and Scottish broadswords (from social events) seem to be the best, so I don't feel like I'm missing out on too much.