Understanding iotop
Look at this question: https://unix.stackexchange.com/questions/282225/how-does-iotop-calculate-the-relative-i-o-activity.
The IO column shows the percentage of the process time that is spent waiting on IO operations. So it is not related to a global usage of the disk.
You pointed out in the comments that your disk is reading at ~130 MB/s. I have a 5400 RPM HD here and I benchmarked my system partition using gnome-disks and could not get more than 100 MB/s when reading. So maybe your disk is not being able to handle all that load and that is why the query is slow.