Code credit: Mark Jaquith (http://markjaquith.com/)

exclude-theme-update.php

<?php
//* Do NOT include this comment or the opening php tag above


//* Don't Update Theme
//* @author Mark Jaquith
//* @link http://markjaquith.wordpress.com/2009/12/14/excluding-your-plugin-or-theme-from-update-checks/
add_filter( 'http_request_args', 'cws_hidden_theme_12345', 5, 2 );
function cws_hidden_theme_12345( $r, $url ) {
    if ( 0 !== strpos( $url, 'http://api.wordpress.org/themes/update-check' ) )
        return $r; // Not a theme update request. Bail immediately.
 
    $themes = unserialize( $r['body']['themes'] );
    unset( $themes[ get_option( 'template' ) ] );
    unset( $themes[ get_option( 'stylesheet' ) ] );
    $r['body']['themes'] = serialize( $themes );
    return $r;
}