Those few pieces of debris wouldn't mean much even to most scientists, but Khan had two reasons that made him quite confident in his deduction.
First of all, Khan was a pilot. He was no engineer, but the test for his license had included studies about ships' architecture. Humankind had copied those designs from the Nak, reverse-engineering the debris from the First Impact, so Khan's knowledge could help spot familiar details.
Also, Khan had witnessed the crash of an actual Nak ship, and his curse made him relive that experience every time he fell asleep. The nightmares didn't focus on those details, but they existed, and Khan had long since committed them to memory.
The deduction wanted to confirm Khan's hunch about Chuwei's apocalyptic event, but he had limited uses for that information. According to the data in his possession, Chuwei would have experienced the Nak's suicidal attack far earlier than humankind, making any debris a few millennia old.