Pruce smelled a lot of bullshit, but Link's confusion looked genuine enough that it gave Pruce a moment of his own confusion. Especially since that explanation contradicted something the queen had said, but Pruce couldn't imagine that Link wouldn't know that he had a piece of something as powerful as the Triforce was supposed to be.
Maybe he didn't, but the queen seemed to have known.
"That'd make a whole lot more sense if she hadn't said that you can both be aware of each other," he said, fishing for either a reaction that told him the line about the Sword was total bullshit, or an explanation that held up Link's story to scrutiny. It'd be tough for Pruce to tell if it didn't on the technical level, he didn't know anything about this Triforce thing, but he could still recognize bullshit when he saw it.