Efficiency is the main difference between the two. Qualitatively you can tell because the coarser pitch (48 vs 64) is noisier. Noise is energy lost (just as heat, etc). To control noise the only thing one can do is adjust play between pinion/spur. Loud noise indicates too much play.
But the story is more complicated than that.
A finer pitch has two ways of improving efficiency. First, at the same diameter the finer pitch will have more teeth, so you gain torque. But that's not the comparison most are interested in, since what we want is to know is which is more effcicient at the same gear ratio. This means a 64 pitch spur will have a smaller diameter, but the pinion will have a smaller diameter too. The ratios of these diameters can be used to compare the torque between using 48 and 64 pitch, and 64 pitch comes ahead.
The tooth profile is important too for efficiency and as far as I can tell the tooth profile is identical on the spur and pinions in 64 pitch whereas on 48 they're not. Backlash (american) or play is another important factor (very important actually) in efficiency and here 64 wins again since the smaller teeth allow for a closer engagement (smaller play) which in turn gives better efficiency.
All that is rather academic unfortunately since the general efficiency of spur gears (straight cut teeth on wheels) is between 98-99% irrespective of pitch, etc. So the best you can hope for is an advantage of 1% over your opponent. This is why other considerations come before efficiency as has been demonstrated already by previous posts.
My personal preference is to run 64 pitch, but I am mainly running TC on carpet, indoors. I have however converted some of my offraod cars to run 64pitch but they have enclosed gears, so there is no problem with dirt, etc. I have never had any problems at all whatsoever with it (I use Kawada pinions and spurs) and the part I like best is that my car is silent as a ghost on the track.