Interesting post. I can only respond to improperly ejected disks upon sleep and disks not showing up in Finder or DU upon wake.
I have a 2014 MBA running 10.9.4 using 3 different USB 3 drives. Every time, upon sleep, wether its normal sleep or hibernate, the disks will improperly eject and often cannot be remounted without a restart, occasionally, 2 restarts. If I connect the drives to an older usb 2 MBA running 10.8.5, they all run fine using the same cable. Using a powered external usb port makes no difference, once sleep is effected, the drives disconnect.
Things I tried:
Now on third OWC (2 models) usb 3 drive and 5 different usb 3 cables - no difference.
Borrowed a Seagate usb 3 portable from a friend - no difference.
Disabled Hibernate - no difference.
Uncheck put drives to sleep - no difference.
Never sleep - works but not acceptable to me.
Using a usb coupler with a usb 3 cable and drive - no difference as well as unacceptable to me.
Install Jettison version 1.4.1d3 (beta) - works, earlier version did not, get it from the developer.
My experience and from reading the thread is this is an OSX issue with no eject command prior to sleep, usb port power being turned off upon sleep and, perhaps, no record of the drive having been there upon wake.
As a bandaid approach Jettison solved my problems. For the long-term, I've put 2 new Macs on hold until this issue is resolved as moving from usb 3 to Thunderbolt does not appear to solve the problem. This is a very common issue affecting purchasers of late model Mac's. If enough people would simply delay their Mac upgrades or return them the minute they run into the problem (the first time a usb 3 drive is connected) then perhaps Apple will start reacting. Or, try Jettison. Apparently a small 3rd party developer can fix OSX and Apple cannot or does not bother trying.