Yes its intentional 
some missions can't be taken again until some time has passed and some are once per campaign (most notably the extremely simple tutorial missions for new players such as "get a royal marriage").
Not sure what you mean with an "extra" waiting time though. There is one timer on the mission and an unrelated duration on the reward.
Once your reward has run out you can still get the same modifier from other missions, not just this one.
Edit: and as I missed part of the question the reasons are to preserve variety and to avoid cycling the same missions.
some missions can't be taken again until some time has passed and some are once per campaign (most notably the extremely simple tutorial missions for new players such as "get a royal marriage").Not sure what you mean with an "extra" waiting time though. There is one timer on the mission and an unrelated duration on the reward.
Once your reward has run out you can still get the same modifier from other missions, not just this one.
Edit: and as I missed part of the question the reasons are to preserve variety and to avoid cycling the same missions.
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