Seems like a variety of problems dog-piling onto this post. I was having two related problems I reported here a while ago: 1) My drives would spontaneously eject and 2) they would not re-mount after the computer woke from sleep, but Finder thinks they're mounted and chaos ensues.
Somewhere along the line, the spontaneous ejection problem went away for me--not sure what I did to fix that but it might've happened as a result of repairing the drive in the disk utility. The other (and more significant) problem still remained (drives remaining unmounted after computer wakes from sleep, but Finder thinks they're still mounted.)
My specific setup was a 2T Western Digital black and a 4T Wester Digital black drive in an Icy Dock dual disk enclosure set in JBOD mode (meaning it's just two separate drives.) The interconnect is USB3. I was using the 4T drive for time machine and the 2T drive for storage.
I did several experiments with different drives in different enclosures (including a couple of 1T drives I have) and finally narrowed my problem down to a specific 2T Western Digital Black drive. If I removed that drive from my system, my other drives would be happy and reliable regardless of other system variables. Conversely this 2T WD Black drive would get stuck after wake from sleep no matter which external enclosure it was in. I even caught it misbehaving in a Firewire enclosure once.
I bought a 4T Seagate the replace the 2T Western Digital and the problem is, so far, gone. So now I have two 4T drives--one WD and one Seagate. As a bonus, I noticed both drives are a lot faster with the 2T drive gone. I didn't get Seagate for reliably reasons (Seagate is the least reliable brand according to Backblaze)--I only got it because it's different (and it happens to be very inexpensive as well.) Besides, even the least reliable drive is still very reliable.
Another thing I discovered was my 4T Western Digital drive had gotten quite corrupt over the last several months--probably as a result of all these nasty disconnect problems. It was so bad that the disk utility couldn't repair it. Reformatting it cleared the problem and had the added bonus of making the speed far greater (it was previously running about 60MB/s and now it's up at 150MS/s). So there's might've been something going on there as well.
Again, I think this problem we're all posting about isn't one problem. So what I didn't may not help others.
So in Summary: 1) try removing and rearranging individual drives from your setup and see if your unmount/wake-from-sleep issues are related to just one of them; 2) repair the drive in disk utility (and if that fails--reformat it.)
Another tip is sometimes a drive needs to be formatted in the enclosure it's in to work reliably. I had this problem with my 1T WD black drive once.
Another thing some brave folks might consider trying is the Yosemite public beta. Who knows, maybe that'll clear the problem. If the problem still exists there, then at least you'll probably get more attention when you report the bug.
Bart