I've put a ton of thought into this myself. I haven't posted a work log or a build yet (been too busy actually doing the build itself), but since I have a soft top Jeep, and Jeep hasn't figured out how to make a soft top that doesn't leak yet, I had to come up with a rugged and secure solution myself. I ended up going with Pelican Cases. All components are mounted into Pelican Cases with bulkhead connectors providing the interconnect. Peltier type thermoelectric devices provide active cooling to the entire box. This way, the boxes are waterproof, cooled, and secure (bolted down and cable locked).
Outside of what I've done, it may be difficult to find a happy medium between keeping the condensation off and allowing the case to cool properly. Is your vehicle open? I haven't heard of anyone having issues with condensation with a standard, closed vehicle. Does it mess with your existing radio?
Maybe you could try laying a breathable fabric over the case, like cheesecloth. It would let the heat out but keep the moisture off....? Possibly. But don't quote me on that one, it's just an idea.