Short answer: yes.
Especially if you put low bars like clubmans or clipons. The extra cable will cause improper routing and can cause the cables to bind or break over time. You CAN route them differently to try and take up the slack, but MotionPro will make you custom length cables for an affordable price.
I had a GS550 not long ago that had MX bars on it, and the cables had not been shortened. The choke cable was broken from a tight turn it took leaving the handlebar, and the clutch/throttles would bind depending on where the handlebars were positioned.