I spoke with the author of the site about a year ago now, and his answer is that there is no true way to delete items, and having such a large database has never affected performance, so it's never been implemented. Fragswapper has been up since 2006 and has never required a fee to use.....and the ads on the site only pay for the hosting for the site. He also said that he has started rewriting it, but because it doesn't actually generate any revenue for him, it's tough to justify the 100's of hours it'll take to rewrite it. It's been started, but has no projected completion date yet. He estimated that if the time taken were billable, it would be in the neighborhood of 10's of thousands of dollars to complete.
I thanked him for what he has done with the site as he does continue to provide support for it, and that was the end of the conversation.