In general, shorter pins tend to read the lane sooner and have a more even reaction. Longer pins tend to go a little longer with a little more backend reaction. As others have said, drilling options may be limited with extremely short or long pins. Drilling a 5+" pin ball stacked leverage (pin and CG 3 3/8" from PAP) may require a monster weight hole. Likewise, you probably couldn't do a pin-axis drilling (pin-on-PAP) with a 1/2" pin unless the top weight was stupidly low (which is probably fine anyway).
As far as the difference between a 1-2" pin Tsunami and a 3-4" one, a Throwbot might notice a difference in reaction given the same drilling, but since the Tsunami has a PSA (the second pin about 7" from the primary one), the CG location and pin distance should have a fairly small effect.
SH