i would recommend a laptop for simplest setup. but if you're really thinking about a desktop computer, consider two approaches:
1) cut a rectangular hole in the work bench surface, cover it with a lexan or plexiglass cover and build a mount for the computer monitor underneath with keyboard tray and computer unit. this way, your entire workbench surface is still "open" and you don't have a computer in the way when you need to lay down a long or large object.
2) instead of on the work bench surface, consider checking out ergotron products so you can mount an arm on the side that can hold a LCD display and a keyboard/mouse. then run the wiring down the arm to your computer that you can conceal somewhere else. again, by doing so, you don't have the computer stuff sitting on your work surface.
just some thoughts.... but require some work and money. a laptop would be simpler way to go and you can dedicate a drawer to it and just put it away when you don't need it.