As the answers above say, the diameter of the well is usually included, but if this is the case, the measurement will never be zero, and the diameter of the well can vary. For these reasons, we always subtract the well diameter from the measurement, but this must be made clear in the Methods section.
Conventional not to substract the well diameter any more than the disc diameter. One must execute the method to obtain a consistent well. Suppose folks in their own lab can use any internal protocol they wish but it's tough to measure the radius from well out and how many such are measured? If wells are so irregular, maybe use an Oxford peni cylinder. and measure diameter.
Article Well diffusion for antifungal susceptibility testing