Here's a theory on that: It was stolen, but crashed. Pilot error.
Plausible, but not neccessarily the highest probability. The cropduster was configured for a ferrying trip - using large internal and external tanks for fuel. It had a VERY long range, much much farther than any conventional light plane. It could have made it to Mexico or Central America from the island (forgot which) it started from. Then again, as you point out, the person who stole it might have not known how to switch fuel tanks and had to ditch in the middle of the Gulf of Mexico. Weather was mild at the time the plane disappeared.
I would also say it is likely that, just by the number of arrests made after 9/11, we messed up the schedule on at least a handful of ops under way.