I run plasma and spindle on my pro 48x48. Have for about 7 months now. I run the CNC Router Parts setup with dual z-axis. Works REALLY well. I don't cover my spindle, maybe should. It has some spots on it from mild splashes, but that's about it. Nothing I've needed to worry about yet.
One thing you may run into is interference from the torch on your prox sensors. I've grounded my machine according to Hypertherm's specs. I run the plasma cable as far away from other wires as possible to reduce electrical noise, but I was still getting false triggers of Z and X limit switches. Usually during the piercing when the plasma first fires.
What I ended up doing is turning off my limit switches. They are still there for homing AND they will still stop me when I am moving the machine manually, but not when the machine is running g-code. I always check my limits before I start anyway.