This isn't really a software question, but ok I'll bite.
It wholly depends upon your personal aesthetic sense and what kind of interface you are using. A lot of us (read myself) are purists and don't like admin buttons on our control panels. Any additional buttons we might need are hidden inside the coin door and/or we have a keyboard stuffed in there for changing settings, ect..
Your most popular keyboard interfaces, the ipac and keywiz, both have shifted functions support. So I don't need an exit key on my cp, rather I can press 1p start and 2p start at the same time to exit. The same goes for any other admin buttons you might need.
A joystick hack or something similar obviously isn't going to have this BUT in the case of mame and only mame, you can define hotkeys to functions inside of mame as well.
So you have some options.
Also... do you like the neogeo games a lot? If so you might want to consider 7 buttons per player (bottom row three buttons with a 4th down and to the left of the first button, and 3 button on the top row) as it makes 4 button fighters easier to play. It's also helpful for the run button for mk3.