Good question. I can only offer more or less plausible causes:
Predator B was designed from the outset to carry weapons, as such the large inverted-V tails might have gotten in the way of the exhaust of powered munitions. Or maybe the structural integration of the turboprop engine worked best with the V-layout, but I doubt. Either way, flight qualities are probably the same provided the vertical and horizontal projected areas are the same. there might be a trade in spiral stability vs dutch roll, but i doubt you would really care, with an autopilot taking care of things.
It is interesting to note that the earlier GA Prowler had the opposite arrangement (inverted Y?)
Any other ideas?