Unless the seller has a recent slip from a Canon service center, there is no way of determing the shutter count on a 1d3. Those programs that try to estimate are not accurate, and usually will have an estimate of <10k. I had a 1d3 with well over 85k actuations that all the programs had listed at 7k. If you see a seller listing a 1d3 that is all beat up, but they tell you it has 6k actuations, be skeptical. Anyone can make up whatever shutter estimate they'd like when selling (since it's hard to accurately verify), so don't buy on that bit of information.
I would pay more attention to the condition of the body and signs of use (fading, brassing, etc). Find a body that is in good shape, and more than likely the shutter count will be lower. It's hard to get over 100k on a shutter without some signs of use appearing. I also find that people who keep their original boxes/accessories, etc, tend to keep better care of their gear, so keep that in mind.
Frankly, for the 1d3, I'd prefer to see a body with a higher shutter count. These bodies are getting to be 4 or 5 years old now. If it had a low shutter count, I'd probably wonder if it from lack of use due to recurring AF issues, etc... Getting a well used body, you'd hope that nobody would put 100k actuations on a body that sucked at autofocusing!