Why does merlyn say the nunc dimittis in the queen of air and darkness?

Because Arthur has come to the realization that might can only serve as a instrument of justice, and thus he will order his kingdom by the principles of justice. This is the reason why Merlyn has been teaching Wart (throughout the book The SWord and the Stone), and thus he says the nunc dimittis which is the final prayer of compline, which translates"Now you may let your servant go in peace, your Word has been fullfilled. My own eyes have seen the salvation you have prepared in the sight of every people: a light to reveal you to the gentiles and the glory of your people Israel" referencing both the fact that he has accomplished his task (so he can go in peace) and that Arthur is a Christ-like figure.