I could understand that the definition of a second wouldn't have an uncertainty when related to the transition of the Cs atom, so it doesn't have an error because it's an absolute reference and we measure other stuff using the physical definition of a second, like atomic clocks do.

But why doesn't the speed of light have uncertainty? Isn't the speed of light something that's measured physically?

Check out that at NIST.

The second and the speed of light are precisely defined, and the metre is then specified as a function of $c$ and the second. So when you experimentally measure the speed of light you are effectively measuring the length of the metre i.e. the experimental error is the error in the measurement of the metre not the error in the speed of light or the second.
It may seem odd to treat the metre as variable and the speed of light as a fixed quantity, but it's not as odd as you may think. The speed of light is not just some number, it's a fundamental property of the universe and is related to its geometry. By contrast the metre is just a length that happens to be convenient for humans. See What is so special about speed of light in vacuum? for more info.
