Testing the drive on the internal bus will tell you whether its the drive or the sonnet card which is at fault. Seems like the best place to start. If the drive doesn't show on the desktop, use Disk Utility/Diskwarrior/Techtool to see if they can spot it.
If not, talk to WD about a replacement drive. If it shows up, it must be the card, so talk to Sonnet. If the card used to work under OS 9, then I can't see that upgrading your X install to 10.3.8 should have any effect on its functionaliy under 9. If they don't tell you otherwise, ask for a new card.