I think those two HDD are very heavy

Heavy capacity, with all the programs software you install and files you download. Your hard disk, each have Win XP correct? Though your system requirements are very good, your computer probably was too busy in maintaining those two HDD at the same time.
You can try and error by only running one of your HDD as primary master and see what happens when shutting it down. I'm sure its even faster.
Your computer probably needs a lot of juice from the power supply as well. Why don't you have only one OS for your primary master? Instead of having it in two each. The other HDD would be your primary slave. A lot of people usually updates their Win XP. Its got a lot to do with RAMs.
p/s: I never update my Win XP and currently running 2 HDD as well. All seems fine but only takes mere 7 seconds to hibernate and shutting down takes mere 12 seconds. That was just a rough guess but mere that