My guess is they are tied to your gamertag. I think people who wait for the retail version will get a crack at the elusive targets provided they haven't already played the game on their account.
This way it works out how IO wants. Everyone gets one chance at it. But there will be no workaround where you can simply buy a physical version to go with your digital copy.
I do believe they mean it when they say they are one time hits. It would lose all tension if it was going to be recycled in the future. Everyone could simply relax and wait for the next cycle if that was the case.
The reason why I believe new gamers next year will get a chance is because it would look silly to start up your game only to see you already failed to get some challenges and rewards from day one.
But any gamer who already activated hitman on their gamertag account will be stuck with whatever result they have: failed, passed, missed.