Yup, you can make an excellent control panel either with or without plexi, so it mainly just comes down to personal taste. Most of my time in the arcades was spent in the early to mid '90s, so I pretty much only remember playing games with plexi covered CP's, which is why it feels more authentic to me to have plexi on the CP. Many members here will tell you they have the exact opposite memory, so they didn't want to use plexi.
Both options work well, so you just have to decide which one would make a more authentic arcade experience for you.