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The Kindle has a built-in function for deleting books (detailed in the manual). I don't think you can delete books from the Kindle via Calibre.
You can put hundreds of books on the Kindle without affecting the performance much. The only gotcha is that when you put a lot of books on at once, the system can bog down while indexing them for the search function, so its best to put them on a few at a time.
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