The center of a golf ball most certainly affects its bouncing properties as well as it's outer shell. Good observation! A ball's bounce relies on it's compression (how much it deforms/compresses when an impacting load is applied - like when the club face hits the ball or the ball bounces off a cart path) and it's hardness (how much it's outer shell indents when a constant load is applied - like when the ball is rolling on a fairway or green). The following sites provide probably more information than you ever wanted to know about golf balls:

The things that determine how far a golf ball bounces are it's starting speed, and what kind of surface it's bouncing on, and what direction it starts going, such as straight up or just a little above the ground, and maybe a little of other things too.