The height of the exhaust pipe does not affect engine tuning or anything of that sort if you decide to shorten it. Be sure to put an exhaust cap (flap) on the end to keep out the rain. Tractor Supply has them and probably most tractor dealers.
However, if you do hacksaw off the pipe be ready for a face full of exhaust soot if the wind is blowing in the right (wrong) direction. Also, it will happen at speed.
My L48 and BX2200 have the exhaust by the left front tire. That is hardly ideal either if you are thinking of that kind of modification.