Its not just links, they take into account many other things, if all of the 1000 links are reciprocal links with PR 0 or N/A. To google that does not mean much. But the site with a PR 3. Probably has one way links that have high PR's, like 3 and 4. And they also base it off of traffic.
Hard to say that it's accurate because of frequent changes of it's algo and besides no system that is 100% bug-free.
Over the past year one site of mine has gone from PR4 to PR2, yet traffic is way up and sales have tripled. Am I worried about my PR? I don't think so!
I think it is accurate. Most of those who say it is not accurate are either banned by google from adsense or failed to get a toolbar PR they expected for their site.