why would you want to mount your carPC to your sub box?
I don't think the sub itself would "wreck" your HDD, but having your carPC mounted to a 'loose' sub box (the box will bounce around when you hits bumps) might damage it. another issue would be theft. if some d****bag breaks into your trunk/boot and steals your subs then you automatically lose your carPC with it. I'm not saying they wouldn't steal it anyways, but there's no point in making it easier for them.
it would be better to mount your carPC to the car itself. it can still be in the trunk/boot, just not on the sub box itself. many people have their carPCs near/next to subwoofers. I ran mine like that for months without a problem. the HDD I used was about 6 years old, and it still works good to this day. I haven't read of any HDD failures as a direct result of being too close to a subwoofer.
mounting your carPC in the trunk/boot works fine, many members here have their systems mounted there. it's a bit more of a pain because you need to run VGA and USB extension cables, as well as extra long wiring for power, ACC, audio, etc. I'm not telling you not to mount it there, but I would suggest looking at other locations as well, and weigh the pros/cons of each location carefully before you start building everything.
as far as cases are concerned, we can't recommend a case until we know what components you will be using (motherboard, HDD (2.5" or 3.5"), PSU, etc).