My experience is not exactly the same as what I have read here, however it may be of interest and of help for someone having hard drive problems.
I have a large itunes library living on a WD 1TB portable My Passport (USB 3) external hard drive.
If I left my MacBook / Mountain Lion running over night or for extended periods, the external drive would go missing-in-action. iTunes would be unable to see to access the external drive. If I tried to play a song or a podcast showing in iTunes it would not be found and iTunes would ask if I wanted to locate it. If I said yes and tried to point to the external drive, the external drive would NOT be showing in finder.
Disk utility could not see the drive to mount or to repair.
A restart would not reclaim its existence.
I could shut down and remove the external USB cable and plug the drive into my secondary iMac and it wouldn't show to mount sometimes, and sometimes it would show. When it would show, I would run disk utility-repair on it and all seemed fine, so I would unmount it and reinstall to the MacBook; StartUp and everything would be cool until an extended period of time passed, and again it would go missing-in-action.
I found if I just shutdown and waited five or ten minutes to startup, the missing drive would miraculously reappear and seemingly be healed until the next time. (Now I think this rest period in effect was a power cycle of the drive, when I would remove and mount on a secondary computer sometimes it would be too quick for the drive to reset and therefore would still not be seen to mount yet)
This freaked me out; not knowing when the fatal failure would occur. Over time I bought two more 1TB external drives to backup and cover my posterior with double redundancy. Even backing up to one and wiping and reformatting fresh did not resolve the missing-in-action condition on the backup drives either.
Since it happened to multiple drives, I figured the problem to be with something in common, which pointed to Mountain Lion. I was hopeful the recent Mountain Lion Update would provide the remedy. Sadly not so.
This has been going on for months. Really frustrating. Finally I thought to check with Western Digital for any firmware updates. Hooray there is one dated mid 11/14/2012. After completing the update, I seem to be free from this scary and annoying drive gone missing-in-action after extended away time.
The firmware update notes "Made device detection more robust."
Hopefully this post can help some who have been having hard drive issues.