Assuming you are getting it remapped to suit the new header the tuner will turn off the secondary O2 sensor monitoring and you therefore don't get an EML.
If you're replacing the manifold on an already mapped car and it had a cat on when originally mapped, then the mapper might not have turned off the secondary O2 sensor monitoring because it had a cat. Do you see what I'm saying? If that's happened then you will get the EML on, but the car needs remapping in this circumstance anyway.