I suspect that they use velocity for two reasons:
- As the integral of acceleration, i'd expect it to be a good deal less noisy than raw acceleration - which then makes it much easier for a human to interpret.
- What they're actually interested in is displacement (from the link above, displacement is what gets used whenever the engines aren't at idle). Large acceleration doesn't matter much (and may even be normal) as long as it's only occurring over a very short distance. In this case you'd expect the velocity to be small (over a short distance, even at high acceleration there's not space for a large velocity to build up). On the other hand, vibration over a large distance (even if the peak acceleration is small) suggests that something is loose. In this case the velocity could be substantial, since even at a small acceleration over a long distance will cause a high velocity.