Whoa, back up a second here... there's a FOURTH bolt?
I just looked and by god, you're right! None of my hinge pockets have any trace of ever having a captive nut, but that's a minor point compared to just exactly how would one go about putting that bolt in? Things are pretty cramped in that pocket with the hinge in and I'd be willing to bet that bolt got left out of a lot of repairs.