Page numbers are stored as a file on the kindle called "[userstore]/documents/{book}.sdr/{book}.apnx" (where {book} is the filename minus the extension of the book itself).
calibre will by default generate and send these when sending a book from your library to the device -- but as Little.Egret warned, they are calculated through guesswork. You can increase the accuracy of the guess by using a custom column to hold the page count. (See the options in the device driver.)
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