I've thought about this from time to time. I built a Moon Patrol cabinet about a year or so back, and it had dual handed controls. Was an interesting experience, and got me thinking.
Speaking as a long time right-handed Street Fighter player, I've seen players play "crossed over" so their right hand is on the joystick, due to the complex inputs required for that game. I used to struggle with it in my early years, but over time my left hand just got more co-ordinated with practice.
Should we make control panels different for lefties? I dunno. You could argue it will mess them up if they go and play games somewhere else. You could also argue that almost every game console and arcade in the world is pretty much designed for righties, and that's not fair.
I'm more inclined to say - stick with the standard, so that they get used to it, and can play arcades easily elsewhere. With that said, if they're likely to never play a real arcade machine outside of home, then I guess it doesn't matter so much.