So, just another idea. I could put a bigish BeQuiet cooler on my CPU, cut a hole in the case lid (will build my own case from aluminium sheets), and let the heat-sink/fan sit above the case. No dust will touch the motherboard, and airflow will be great.
My worry would be that, in a backpack, there would be nothing to protect / support the cooler. Maybe I'd need a second case to go around the cooler for travelling.
I'm thinking any of these coolers would work well.