On my modular panel (link below) I have both - there are three buttons on the trackball panel, as well as button panels to either side (as desired).
In reality - I almost never use the buttons above the trackball, and instead use the button panels on either side. If I were building a dedicated trackball CP I would mount three buttons on each side of the trackball - to support both left and right handed players.
You also might want to consider a single joystick if only to switch games. Some front ends have joystick support but don't let you select games with the trackball.
I've used 1/2" MDF on all of my panels and it works fine as long as it is properly supported.