Long tubes are better for high rpm trucks, Shorty's are generally a low end option, depends where you want the power advantage in your exhaust
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Quite the opposite, actually. Long tubes have much better exhaust scavenging at low RPM's due to the length of the exhaust pulse relative to the length of the tube. The longer tube and larger collector helps to smooth out the pulse timing differences between the cylinders and keeps the velocity of the exhaust gas higher to make up for the lack of volume. This helps in low RPM torque production and midrange horsepower. A tube that does well at low RPM's will generally not do as well at higher RPM's, as it becomes a restriction to flow. It's similar to siphoning water out of a tank. Once you start the flow, the movement of the fluid creates a low pressure zone in the tube that pulls more fluid out of the tank. If the tube is too short, there won't be enough inertia to create the low pressure zone, so the flow stops until you siphon some more. Now if you put a pump in the tank ( similar to increased exhaust flow due to higher RPM/bigger displacement/etc ) that same tube becomes a restriction to flow. Now, a shorter, larger diameter tube would be more beneficial to keep pressure low and create the least restriction to flow possible. This example doesn't address pulse timing, wave tuning, and a host of other topics related to exhaust design and fluid dynamics, but you get the idea.
For a heavy 3/4 ton 4WD truck with a big-inch engine that rarely sees high RPM (by this I mean 4500-6000), and may not have the clearance for long tubes due to the drivetrain, shorties are the way to go. Not to mention the pricing. Shorties my be initially more expensive, but you'll bypass that with the price of modifying the exhaust for the long tubes and clearing everything. The cam choice is important as well. Unless you're going to run a considerably more aggressive cam, there's not a huge difference in either one, but the shorties are much, much easier to install.
If you want easy installation and next to no exhaust work, then shorties are great. If you want dual exhaust regardless of your choice, then the exhaust work argument becomes moot, and it's down to cost, performance, and installation. If you're buying quality units to begin with (such as your Kook's) then cost difference really isn't a huge issue either. That leaves performance and installation. Those are a toss up and wholly dependent on what you value the most: maximum performance or ease of installation. I lean to the former, you to the latter. We can agree to disagree. As it turns out, there aren't any long tubes readily available for a '99 K2500 with a 7.4L. So it's manifolds, shorties, or custom headers.
