Admin Notices coding standard issue

One way you can handle this would be to do the wp_sprintf when assigning the value of the $message variable and then use wp_kses when you want to output. You could also output the div and paragraph tags before and after the message, which would eliminate the need for wp_sprintf in this instance.

add_action( 'admin_notices', function() {
        $message = __( 'We suggest that you use the <b>API Key file</b> for your API Keys.', 'package-wordpress' );
        echo '<div class="notice notice-warning is-dismissible"><p>' . wp_kses( $message, array( 'b' => array() ) ) . '</p></div>';
});

If you wanted to keep it closer to the original you could do something like:

add_action( 'admin_notices', function() {
        $class="notice notice-warning is-dismissible";
        $message = wp_sprintf( __( '<div class="%s"><p>We suggest that you use the <b>API Key file</b> for your API Keys.</p></div>', 'package-wordpress' ), $class );

        echo wp_kses( $message, array(
            'div' => array( 'class' => array() ),
            'p' => array(),
            'b' => array(),
        ));
});