Kicker makes a "Free Air" sub (other manufacturers too, I'm sure) that's supposed to be really good for this kind of application - as long as the trunk is effectively sealed off from the cab, it should sound pretty awesome - uses the whole trunk as an 'enclosure,' much like the 6x9s in a rear deck would.
I remember in my '82 Mustang hatchback, I made a cover for the entire hatch area with 2 Clarion 990 6x9s - no enclosure, and they sounded awesome. After learning about the bass response of subwoofers in enclosures, I decided to make a box for the 6x9s under the cover, and to be honest, they sounded like crap afterward. The Free Air subs use the same technology as the 6x9s (probably a different magnet & voice coil make-up, resistance, and reflexive fastener for the cone-to-basket attachment), so I'm guessing they've gotta be pretty good. Check the specs on the Kicker Free Air subs against their Competition line, and I think you'll see they are comparable - without needing enclosures. Running one of them "out of phase" can have some really interesting effects as well - that's how the Kicker Comp 8s in a single enclosure are wired in the Jeep... and they hit hard (with the roof on, that is - still not too bad with the top off as well... just the obvious reflective loss without the roof).
Hope that helps.
