I've narrowed the search for the cause of this problem down slightly by running some crude tests.
Replacing the following kexts with older versions stops my disks disappearing after using a sleep/wake cycle.
AppleAHCIPort.kext v2.4.0 from 10.8 DP1 replaced with version 2.2.0 from 10.7.3
IOAHCIFamily.kext v2.2.0 from 10.8 DP1 replaced with version 2.0.7 from 10.7.3
It's not much, but it's a start.
Next step is to look more closely at these kexts to find out more.....
Thanks man! This worked fantastic. Now I can wake from sleep with no problem.