The cycle counters are a just monotonically incrementing values, so polling them just lets you calculate the average effective frequency over the poll interval.

The cycle counters are a just monotonically incrementing values, so polling them just lets you calculate the average effective frequency over the poll interval. You're right that stuff like i/o might happen in different numbers of cycles depending on actual frequency, but those operations generally take the same amount of wall time either way, so it comes out in the wash.