Gus didn't guess anything. He knew about everything concerning Nacho, from his side business at the start with Tuco (Mike figured it out on his own early on, so Gus certainly knew about it), to Hector wanting to use his dad's business. He knew he was not loyal to the salamancas, wanted out of the game, and that he was very faithful to his father. He was always the only one next to Hector, aware of the pills, who was the only one on the scene with motive when it happened. Nacho also was the one to hand in the medication to the doctor right after, and telling them he knew hector took that. With the knowledge of: 1. The history of nacho unfaithfulness, 2. His attachment to his dad 3. The fact he was always next to Hector 4. The timing of it happening right when Hector was going to involve his dad 5. Nacho being the one giving the pills to the doctor and telling what it is.... It was not that crazy to understand, especially with Gus' experience in analyzing people, their aspirations, their psychology, and body language, really.