Arthur has always known that Merlin has magic.
It's not something that he consciously thinks about or has even considered. But there were too many odd, whispered words. Too many coincidences. Too many sudden disappearances and reappearances. Too many moments where Arthur spoke angrily of magic and its users and Merlin wasn't quick enough, hurt flashing in his eyes before he tamped it down. There were too many times when Arthur looked into Merlin's face, lips parted and face flushed with pleasure, and thought he saw Merlin's eyes change gold.
Why else would he turn to Merlin when wavering about magic's being good or bad? Why else would Merlin have such stores of knowledge about the Old Religion, its rituals and spells and curses? Why else would he know, even before he asks Merlin a question about magic, that it will hurt Merlin to answer?
But he never thinks it over. All of those facts are filed away, deep inside of him, right at the bottom of his soul where he carefully places them in a trunk and locks them, waiting for the key.
The key, in this case, being Merlin's admittance.
But Merlin will never admit it, and again, part of Arthur knows this. Merlin loves him, loves him in a way that scares Arthur sometimes, because he knows that if there was an arrow speeding toward him and Merlin had no other way, he'd jump in front and take it himself. He's already drunk poison for Arthur, back when he barely knew him and hardly liked him. He's lied and stolen and interfered and refused to interfere, all for Arthur's sake. So if Arthur's safety means lying about magic, lying about who he is, Merlin will do it.
Even if it means destroying himself.
Arthur knows this, but he knows it in the way he knows that the sun will rise in the morning: it's a fact, but one you never notice or think about. He knows it in the way he knows the angles and planes of Merlin's body, the lines of his mouth and the light in his eyes. He knows it in the way he knows when Merlin is lying, when Merlin is content, when Merlin is holding something back.
Arthur has always known that Merlin has magic.
But at the same time, he doesn't.