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Yes, getting a "clean" library when you have books numbering in the thousands is indeed a time consuming exercise. Though I would have thought that the time spent on a delete operation vs the time you will have spent opening and comparing all the books to decide which version you want to keep would still not be that significant. You could do what I do of clicking the hyperlink of the next book format in the book details panel, and while waiting for the ebookviewer to display, kick off a delete, task switch to your ebook viewer, make a decision, close and repeat etc. Saves a few brain cycles.
Or you can do what some of us do of having a separate library for the "cleaned" books. Create a new library, then from the existing one use the "Copy to Library" feature to move books into your "clean" library, perhaps by all books for an author at a time. That way Find Duplicates is only dealing with a smaller number of problem groups, your "clean" library will be far smaller (reducing the delete time) etc.
Or else it could just be hardware related - defrag your disk, get a faster drive or even a memory based disk and put your library on that.
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