Watercooling would not work in a car for several reasons. Most importantly, water cooling works by moving cold water over hot parts. Hoewever, on a hot day, the water would get very hot and therefore would not cool well. To make this work you'd need some way to cool the water (peltier cooler, etc) but these generate heat as well...you see where I'm going with this.
Next, in an in-car environment with the movement, bumps, shocks, etc it would not take long for the tubes running the water to come lose, then you can kiss the capruter goodbye.
Better off to move the carputer to a location where there is more ventilation than dehind the dash. Not sure exactly what your interior is like, but is there room under the seats, behind the seats, etc? Those places will get more air circulation, which will help the PC run cool. Apart from that, lots of high quality fans, a good heatsink, etc are things that will help. The EPIA (which I assume is what you're using since you said mini-itx) does not come with a very big heatsink/fan since these CPUs usually don't generate much heat. For in car use, you should look into a bigger/better cooler, then just move as much air as possible over the parts that get hot. Good luck!