I cut the length on mine in half for the same reason. But I left just a little sticking outside the cowl.
Removing the velocity stack will not adversely affect the engine, but, it will probably increase the amount of blow back through the carb.
If you take it off be sure that the carb mounting screws do not penetrate too deep. You may need to use slightly shorter screws.
Only draw back is that with it removed, all of the blow back will be inside your cowl if the carb intake is inside the cowl.