Why didn't the inhibitor chip ever come up on a medical scan?

It did come up on a scan (in the Clone Wars episode Conspiracy), but it took a "Phase 5 atomic-level scan" scan to even see it, and that gave no specific clue to its function.

Even then, it just looked like a small and relatively benign tumour. It's worthy of note that this scan is described as being invasive and harmful to the individual, so it wouldn't usually be used on someone who was sick or injured, let alone someone who had died from a war inujry.

AZI: The scan is almost complete. Everything appears to be normal. Wait a second.

Fives: What? What is it?

AZI: It appears this clone has developed a tumor.

Unfortunately for the Jedi, Palpatine made the evidence disappear at the end of the episode by having the biochip shipped to a medical facility on Coruscant which was under his control.