You're hard drive is specifically designed to withstand bumps and vibrations, so it should be able to handle the subwoofer without significantly reducing its expected lifetime. I would try to keep the hard drive away from the subwoofer as much as possible though, possibly mount it on a rubbery surface or use closed cell foam to protect it a little bit more.
Sound deadening wont stop vibrations from going to the hard drive if they are both in the trunk. Sound deadening would make it worse by keeping all the sound in the trunk and not allowing any to escape.
I've had mine mounted next to my subs for some time. I've had no problems. It's just bolted to the side of the trunk, no vibration reducing tactics used. The shock from hitting bumps is actually much worse than a sub.
I drive a gmc safary my computer is in the center console midle of the front seats in the back there is a wall
with 12 woofers mmats procast and 3 1200w amplifiers the wall is far away by the sliding door of the van and we are on the 155 db
I was looking to move the hard drives to the back but never found a long ide cable so they stay in the case is been a year no problems they are ok