Print WordPress username id inside JavaScript

You can use get_current_user_id() to get the ID of the current user, and in your case, you can do so to print the user ID in the JavaScript Li.re() call:

<script type="text/javascript">
  Li.re( 'ab12','<?php echo get_current_user_id(); ?>' );
</script>

And yes, you can include the user ID as part of a shortcode: (note that I omitted the href parameter for simplicity)

<?php echo do_shortcode( '[mycred_link subid1="' . get_current_user_id() . '"][/mycred_link]' ); ?>

PS: Your shortcode was missing the closing ] tag, so I added it above. All shortcode parameter values should also be wrapped in single/double quotes.