Shorter gears(higher number) does not automatically mean faster. Back in the day when 4 speed transmissions were the norm, they definitely made a difference. But as the number of gears have increased, the ratio spread for the transmissions has grown making the axle ratios less and less important. Now, with the 10 speed trucks, I doubt there is much difference between them at all. The first gear on the 10 speed is so short that you still get a really short gear for getting off the line even with 3.31's.
Also, our engines are so powerful and torquey that it usually overcomes the need to have a high axle ratio. If you had a 5.0 where the torque peaks at much higher RPM, you might see an advantage to higher axle gear ratios.
That said, it really depends on your specific scenario. My truck is a 6 speed trans with 3.73's. When I am climbing a hill with my trailer at 65mph, my truck physically cannot shift to 2nd gear because the engine would go past redline. If I had 3.31's or 3.55's, I might actually be able to drop to second and run closer to 5000 rpm where peak HP is.
So for me, a slightly taller ratio might actually make more sense even though the 3.73's technically provide more mechanical advantage. The key to going fast, pulling a trailer up a mountain, etc is being able to sit at peak HP. HP tells you how much twist an engine can make at the rear wheels compared to another engine. If my Honda makes 200 hp, and my truck makes 400 hp, I can twist my rear tires twice as hard in the truck. But my transmission and gear ratios need to let me reach that 400hp since it only happens in one narrow RPM window.
