This is really a vanilla PHP/HTML question, but for what it’s worth:
<?php if ( $email = get_post_meta( $order->id, '_billing_email', true ) ) : ?>
<li>
<span><?php _e( 'Email:', 'dokan' ); ?></span>
<a href="https://wordpress.stackexchange.com/questions/178783/mailto:<?php echo esc_attr( $email ) ?>"><?php echo esc_html( $email ) ?></a>
</li>
<?php endif ?>
<?php if ( $phone = get_post_meta( $order->id, '_billing_phone', true ) ) : ?>
<li>
<span><?php _e( 'Phone:', 'dokan' ) ?></span>
<a href="tel:<?php echo esc_attr( $phone ) ?>"><?php echo esc_html( $phone ) ?></a>
</li>
<?php endif ?>