Well, one of the advantages to owning a Jeep is there are always plenty of Jeep owners out there looking for parts, so if you get ahold of one with a bad frame, you could always part it out and sell the parts to another Jeep owner who believes they have a good frame....
I am saying if you go mudding or off-roading you will plug any of the drain holes they could put in there anyway. Not much different from the weep holes they put in the rear fenderwells and rockers of trucks.
I suppose it may have benefit to those who stay on pavement.
They put holes in the sides of the frame, so salt and mud could get in, but no holes in the bottom so they could drain, so not sure if that was planned, or just p*ss poor engineering. They probably didn't really care as long as they outlasted the warranty period.