I use two HD's in my SN41G2. I have a 7200rpm 80 gig Maxtor for a primary and a 7200rpm 200gig WD... I have no real problems. I did add an 80 mm fan that blows right on them, just to be sure, but I didn't really need them, so I took them off. I just make sure that I have HD's set to power off when needed. But I ran as a Kazaa server for so long, it never kicked in. Long and short of it, don't worry about it as long as you have quality HD's. But if it worries you, and as long as you have the right Shuttle, make or buy an external firewire/usb2.0 enclosure. I'm getting one for my 200 just for the convenience.
Minolta 50/1.4, 80-200 HS APO G
Sony 18-135mm SAM, 35/1.8 SAM
Tamron Di 90mm/2.8