If like me you have a bunch of external HDDs connected to your system, you are probably facing a similar irritant. External HDDs are configured in firmware to switch to low-power mode within a few minutes if idle. In this mode, the disk spins down and eventually stops. Accessing the disk causes a slight delay as the HDD must spin up again to full-speed and locate the sector on which your data is located.
Apart from the delay, the spinning up of the HDD spindle and raising of the head from it’s parking position to the data area of the disk causes significant clatter and mechanical wear and tear. The S.M.A.R.T. values also get incremented it appears that the HDD was being abused with repeated unplugging and plugging.