If you have a Nios devkit, I recommend adding the Compact Flash component. The CF interface is nearly identical to ATA(IDE), both from a software and hardware perspective. From a hardware standpoint, look at J11 of your devkit. This pinout is identical to an IDE cable. From a software standpoint, the register set required is I believe identical to Compact Flash.
Now, having said that, I have managed to get uC-linux working on my board where I can mount a Compact Flash card. The theory is, if you can talk to a CF card, you should be able to talk to an ATA hard-drive.
Haven't tried it yet though...
Hope this helps,
-Terry