Well, I have a auto map pocket with a New transflective in it. I would not think of removing the stock LCD because I would loose me temperature reading from the climate control. I also use the PC for bigger journeys and not small 10 minute trips to work. You will also loose the radio display and I doubt that you will have a descent radio with the carpc.
In any case it is up to you to decide.
If you decide to remove it maybe you can fit a PC DVD player in there