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I have over 900 books on mine and the slowdown is barely noticeable, so I don't think that's it. However, all those docs you've been deleting probably left entries in the index folder and database, and as others have stated, you may also have one or more documents not indexing properly.
You can delete the index files by accessing the System folder. It's hidden by default, so you'll have to select to show hidden/system files and folders in Explorer if using Windows. Empty the Index folder (but don't delete the folder itself). Then plug your Kindle into a wall outlet and let it index overnight. (Indexing takes a lot of battery power.)
The next morning, use the method in kranu's post above to check for anything not indexed. Those will have to be taken off. If you have calibre, you can do a mobi-to-mobi conversion and then put them back - that usually fixes it. If the problem files are Amazon books, you can just redownload them from your archive.
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