Similar problem here, here’s how I solved the problem.
Try to plug the HD after launching WiiMC. For me it’s working.
When I plug USB and later load WiiMC, HD is not recognized.
When I first load WiiMC and later plug USB, the HD is recognized.
This happens with both USB ports and no matter how I launch WiiMC (it happens both from Channel and from HBC).
IOS 58 is installed (and WiiMC correctly works with it), and I’ve got latest version of channel (1.4) and WiiMC (1.08).