Notchbacks are slightly lighter and slightly stiffer. Hatchbacks have more room and are slightly more aerodynamic.
The hatch would probably make for a better DD just for the sake of being slightly more practical. You can fold down the rear seats and fit a LOT of crap in there. Hatches are also more common (as both LX and GT models were offered in a hatch, only LXs were offered in the notch), and they're usually cheaper.
+1
First Mustang I owned was my 89 5.0 LX. I moved home from college in one trip. I folded down the seats and put a recliner chair, my desktop computer, laser printer, all my dishes, pots and pans, all my clothes, some plastic drawer/boxes, all my bed stuff, bathroom rugs, books, EVERYTHING in it. It was loaded FULL of stuff, mostly stuff you couldn't haul in an open bed of a truck. Took me about an hour to unload everything.
At one point I also hauled home a set of fluorescent lightbulbs in it. They went all the way from the back of the hatch and rested on the dash. I even hauled the entire front suspension beam out of my VW in it, spindle to spindle.
A few years later I was in a wreck and totaled it. But I bought a 2.3L notch and swapped absolutely everything.
I can't even fit a small ice chest in the trunk of my notchback. But I do like the way notchbacks look, and the fact that you don't see many anymore.