I can only guess at the reasons the combat versions were mothballed, but I think I have some pretty good guesses based on my knowledge of the Tundra and its similarity to the Tacoma.
The Tundra takes its entire drivetrain aft of the engine from the Tacoma and other small engine/drivetrain/payload Toyotas...yes, all of it including the transmission...with the exception of the inner CV joints, which are much larger on the Tundra. Factory unlocked rears are identical in the two trucks with the exception of wms dimension...the differentials are identical.
Packed & loaded Tundras weigh in about the same as a packed & loaded 100...three tons. In fact, the engine in the Tundra (2UZFE) is mirrored in several other Toyotas equipped with 1UZ and 3UZ engines, the Tundra takes its engine originally from the LC and similar engines were used in a couple sports cars in different configurations (four bolt mains, different shape to the rods, etc).
I suspect that a packed, loaded, armored, combat equipped Tacoma is NOT light, not at all. In normal use, a Tundra will dump the front differential when the wheels are spun overmuch, it will also dump both inner and outer cv joints and the front halfshafts. The Tacoma has an even smaller inner CV joint. The upper ball joints are very, very small at the neck, and the lower ball joints are sturdy but were swapped later in production for a larger joint and wider footprint. In addition, the spindles' weak spot is near the top where the upper ball joint mounts. While the lower ball joint takes the majority of the shock when the suspension cycles, the tire is outboard of both joints, putting a shear load across the neck of the upper ball joint and a bending load on the spindle when the weight of the truck is over the wheel--more so and much worst when the front end hits the bump stops. It's just the nature of the setup, that's how it works--when the upper joint goes, the wheel flops in to the wheel well, not out. In addition, while the tie rods, steering shaft, and rack/pinion are fairly sturdy, they will not handle constant abuse from things like in-place turns with the brakes locked, side shock loading and other things that are 4WD no-nos. In a combat situation, I can see the stock front end of a Tacoma quickly being overrun...probably a matter of months...not because the front suspension and steering were poorly designed, but because they were meant for highway travel, paved roads, and slow travel over rough terrain, not constant high speed service over rough terrain. They can be built for it, but that costs money.
Back to your original question, I looked at used LCs when I was looking at the Tundra. I found a built LC on 35s, with 4links front and rear, just crazy, with all the interior amenities and a sunroof, 125K miles, asking 35K$. Considering the (easily) 15$K of modifications, it was a pretty good deal. However, I passed because of the plush interior, pretty paint job, completely enclosed passenger and cargo compartment, and all the other amenities that make an LC an LC. It's the same reason I passed on the 330xi...I knew I was only going to get it dirty, scratch the paint, throw stuff on the roof, all things I've done with the Tundra that I don't regret one bit. Muddy boots? Bed. Muddy dog? Bed. Sharp skis and snowboards? Bed. Dirty camping gear? Well, you get the idea. The LC was built for overland luxury. The trucks are built to Git'R'Done. WRT the frame cracking issue, there's a fix, but the first thing is to pack properly--weight to the front, light to the rear. Hanging everything off the ******** end of the truck is a sure way to cantilever weight from the front suspension and overload the frame to the point you need those frame reinforcements. If you need/want a swingout carrier, keep the frame and loading in mind. FWIW Brady's Taco has a near 50/50 distro and I suspect if not for the weight and higher CG it would handle similar to my roommate's S4.
Here is another consideration. Because of the payload constraints of an LC, you'll wind up hucking plenty of things on the roof, or off the back end. I've seen pictures here and other places of LCs with an obvious rear weight bias, cantilevered so bad that the front end was hardly flexing. I've also seen plenty of pictures of LCs with every liquid known to man strapped to the roof, along with the shovel, hilift, recovery ladders, spare tire, kitchen sink, and a few lead weights just to make sure the rig is properly top heavy. This doesn't matter if you're off to the dunes, beaches, backroads and flat dirt, but if you're planning on doing anything other than "light" offroad (ie flat, potholes, no steep climbs/descents, all climbs/descents are level, etc), it's something to consider. If you have someone tugging a tow strap to keep you from rolling because you have everything on the roof (or someone hanging from your bumper), you're on the wrong trail for your packing scheme. It doesn't mean you packed bad, or wrong, or anything, just that the trail you're driving isn't an appropriate place for the way you're packed...and vehicle choice will dictate how you pack. It's not specific to the 100, just an observation for any SUV...I've seen FJCs, 4Runners and Cherokees loaded the same way, with the same downfall.
With a bed, you can put all that stuff nice and low. There's a huge space you can lay out yourself to carry all your amenities and toys, like water at 8#/gal and fuel at 6#/gal...no need to drive down the trail in a skyscraper. It helps the mileage too...throwing it on the roof increases your wind resistance enough to knock the mileage back a few notches regardless the weight. Keeping it in the bed only helps the mileage. In addition, because you have payload space in front of and behind the wheels, you can pack heavy/front to light/rear and acquire a good 50/50 weight distribution and still keep everything in the bed.
Figure out what you want to do most, first, then break it down to SUV vs truck. It's why I wound up with a midsized truck with a generous back seat vs an SUV, and the same choices I made may push you more toward the 100. Of the LC, AC Tundra and DC Taco, the LC has the most comfortable back seat, and IMHO the two trucks had similar back seats...I'd hate to be stuck back there longer than a trip to the trailhead, or as a female friend of mine observed WRT the rear seat of an 00 model Tundra, "it's the most erect thing you'll sit on all night." Not comfortable for adults, but great as an additional storage space. Also FWIW if you look at the lines, a 100 is similar to a reg.cab short bed Taco, but everything is enclosed.
-Sean