Failing hard drives will cause latency spikes for sure, despite appearing to work OK.
Bad PATA/SATA cable can also appear as failing drive, so it pays off to change the cable first.
If you do suspect a failing HDD controller, most boards will have 2 separate controllers, even older ones, so try the other one. Yes, there are many boards with 2 of PATA/IDE controllers, and there are many boards with 2 SATA controllers where usually one does also RAID.