The reasoning behind most people making it shorter is they don't have the funds/don't want to spend for a new can after they crash or what not.
So instead take a few minutes and a couple bucks cut the rashed part off, put together, bam like new.
^Which is understandable.
pretty much what I think when I see a shorty, too cheap to fix it properly!
Armi is right.
The hamonics have to do with where the motor makes it power. Companies spend a LOT of time on R&D to make them work correct for each motor. So why change that.
there is a lot more to it than that though, theres no such thing as a mass produced engine that operates at its full potential, they have to modify and dumb the things down to meet the various regulations surrounding noise and pollution and all sort of other nonsense that are in place in the various world markets they sell the bikes to. - I do see your point though.
I get a tad miffed that people go and spend a few hundred bucks on just a can, and thats it. a friend of mine wants to buy a yoshi can for his R1, its gonna cost him about $300 or so - yet, I found a full Akra exhaust system to suit his bike, second hand and it great condition, for only an extra $200 or so, but he still wants to do just the can.
the way I see it, if you want to make those sorts of changes, do the whole damned exhaust so the elements that comprise the whole system work together properly (rather than just chucking a random can on the end) and rejet/PC to suit.
anything less just seems like pointless blinging to me, and its possible to make the thing run worse when all you do is throw an aftermarket can at it.