Six buttons are plenty for the vast majority of games so this typically comes down to personal preference. The suggestion to make a test panel out of cheaper materials is correct and something you will definitely want to do.
I know for me personally I opted for the seventh button because Neo Geo games are some of my favorites. I also went for the more ergonomic curved layout as fighting games aren't my favorite. None of my friends who are into fighters seem to mind or even notice and can play SFII and the like just fine.
Another thing to consider is what platforms you want to support. If you're going straight MAME or MAME with some old school consoles then a six button layout is just fine. However, if you decide to expand into newer generation consoles or even PC games then there are advantages to having more buttons. For instance, if you go with seven buttons then the seventh (thumb) button can be a shift key that turns your L1 and R1 triggers into L2 and R2. Or, if that's too clunky you can opt for eight buttons although keep in mind the more buttons you add the more complicated and intimidating your panel becomes.
The one thing that ultimately made me decide to go with a seven button layout is using button 4 for A and 123 for BCD makes certain Neo Geo titles cumbersome to play. Take Windjammers for example. That game is super fast paced and making the split second decision to lob vs throw is difficult when the B button is stacked on top of the A button. But yeah, personal preference. My advice, look at the games you want to support, decide how many buttons you think you want, build a test panel, revise, build again, etc until you get it just the way you want it.
The last thing I'll add is if you're adding a trackball you may want to move it down slightly. This puts the P2 joystick out of the way for left and right movement and also gives you more room above so you're not breaking your fingers on the bezel playing Golden Tee.
Hope this helps.