Depending on who you believe, longer pins tend to have less midlane and more backend than shorter pins.  What kind of measuring equipment you need to test that is a different story.

Long pins are more suitable to putting the pin above the finger line than shorter pins, and real long pins, 5+" almost have to be drilled like that to avoid excessive thumb weight.  On the flip side, shorter pins, in the 1-2" range, often get drilled with the pin under the finger line to avoid excessive finger weight.  In both cases, the goal is keeping the CG from getting to far from the centerline.  I believe that a big part of the "longer pins have more length and backend" business is due to the typical drillings used with longer and shorter pins.

There is another difference when you're talking about pins longer than about 4.5".  Those balls are usually considered blems, seconds, x-outs, pro-pins, whatever.  There can be an enticing difference in price when you look for such balls.  Performance-wise, if you're happy with the layouts that long pins require, they're just as good as first-quality balls.

SH