Arthur doesn't know. He doesn't know, but he certainly suspects.
He was a warrior, trained since birth to kill, but also to pay attention and put pieces together. To notice when things didn't add up or make sense. And lately, lots of things weren't making sense.
That first fight in the market, for instance. He would have noticed anything within his path he could have tripped on, and that rope certainly hadn't become so taut by itself.
And Merlin's reflexes were faster than every single one of his knights? He was the one to keep him from being hit by a flying dagger? Really?
Even the small things…how would the worst manservant alive manage to get his armor that clean?
And though he couldn't prove it, it had to have been Merlin who saved and guided him out of the cave, even from his deathbed. Who else would do it…or be able to find him if they wanted to? He and Merlin were connected. He could feel it.
When Gwen was to die and Merlin burst in, insisting he was the one to save her father, Arthur wasn't shocked, scared, or angry like the rest of the men. He finally felt that peace that came when every piece had come together and they were finally forming the image he had known was emerging. He had to scramble to find another explanation to appease his father, but what made the most sense was exactly what Merlin had claimed.
And while it was possible that Will was a sorcerer, Arthur could tell that wasn't what Merlin would have told him. Merlin was shocked, even scared, to hear his friend say it. And, having experience with Merlin's lies, he could tell he wasn't being entirely truthful at the funeral.
While part of him wished Merlin would just trust him and bloody tell him, he was glad to be interrupted before the battle, for the same reason he had not opened that old, red book from Merlin's floor (besides the fact that he had no idea when he had last cleaned that piece of clothing on top of it).
Because, then, he would know.
And then he would have to choose. Not once, but every moment for the rest of his father's life. Betray his father, or betray his friend. Lose one or the other. He did already know which he would choose. But he also knew how it would end. He would either have to send Merlin away, or live in fear until his father eventually uncovered the truth and had Merlin killed. And how would Arthur live without his greatest and most trusted friend?
He didn't know. He didn't know, but he certainly suspected.