Sbzro, I've been working with hard drives since way before they hit the 3.5" or 2.5" formats, and I can't imagine that your bass will even come close to affecting it. Rock on and put it in the trunk. They're not nearly as delicate as they used to be.
Having said that, that don't strap it to the sub enclosure, either! Mount it somewhere where it won't be in physical contact with your speaker system. Sound waves are one thing, vibration is another, but you should still be fine.