After upgrading to 10.9.2 my drives would sleep as they should, that is until I restarted the computer a few days later and the sleep problem returned. Knowing that it was possible for the drives to sleep normally, I spent many hours trying different scenarios of ejecting and mounting drives in order to get them to act normally. Eventually I found a procedure that works. So here's what works for me.
Making sure that no application is using the drive(s), I press the power button on each drive which ejects and shuts them down. I then put the computer to sleep. With the computer still sleeping I power up the drives and wait until they sleep, typically after 10 minutes. I'll then wake the computer at which point the drives automatically wake up and mount. From that point on both drives sleep either when not used for 10 minutes or 10 minutes after the computer is put to sleep. Sometimes I'll have to repeat the procedure doing each drive individually for it to work. Unfortunately, this has to be repeated every time the computer is restarted which for me is not very often.
Note that I have a separate WD drive connected via USB that is used by Time Machine. I've always suspected that TM was part of the problem. As we all now know, USB connected drives sleep noramlly. I also do my backups manually rather than letting TM automatically perform them. At some point I'll try daisy chaining all drives together using FW800 and engage automatic backups to see what happens. For right now though I'm going to well enough alone.
I doubt if this will work for everyone but I thought I'd share it. Perhaps someone with more computer knowledge can explain why this works.
2009 Mac Mini using 2 WD FW800 My Book Studio II. One's formatted Raid 0, the other Raid 1 using WD drive manager.