Buy CDT audio Subs. They need very, very small enclosures but at the sacrifice of needing more power. Check out my thread on my custom Fiberglass enclosure. It would be very easy to adapt something similar into your hatch while keeping everything stealth. I would cut out a sheet of MDF to cover your whole trunk floor. I would then raise it a couple of inches (Enough to fit an amp under there) Assuming your using a 12" sub, I would pull out the spare tire and build your box to fit into that cavity with the false floor sitting above it. Then mount your amp under that false floor as well. Soundproof the heck out of it, and cover the whole thing with speaker enclosure carpet to give it that oem look. Below are some rough pics.
You can even counter sink it and cover it in speaker grill cloth so you won't see the sub.
My setup: