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Al final conseguí solucionarlo, así que por si alguno más le sirve voy a contaros que hice. 

Primero active en el tema la paginación clásica, nada de paginación infinita o con botón, que salgan la cantidad de páginas que hay. Modifiqué el pagination.tpl dentro del directorio  _partials, con el módulo de ofuscar enlaces de winamic instalado. El código quedó tal que así: 

<nav class="bottom_pagination flex_box flex_space_between mb-3 {if $last_page_number && $last_page_number==1} only_one_page{/if}">
  <div class="product_count flex_child">
    {block name='pagination_summary'}
    {l s='Showing %from%-%to% of %total% item(s)' d='Shop.Theme.Catalog' sprintf=['%from%' => $pagination.items_shown_from ,'%to%' => $pagination.items_shown_to, '%total%' => $pagination.total_items]}
    {/block}
  </div>
  <nav aria-label="Page navigation">
    {block name='pagination_page_list'}
    <ul class="pagination">
      {foreach from=$pagination.pages item="page"}
        <li class="page-item {if $page.current} active {/if} {['disabled' => !$page.clickable]|classnames}">
          {if $page.type === 'spacer'}
            <span class="spacer">&hellip;</span>
          {else}
            {if $pagination_jump_to && $is_product_page && !$page.clickable}
              <div class="input-group st_pjump_box general_border" data-url="{$page.url}" data-count="{$pagination.pages_count}">
                <input type="number" class="form-control" name="st_pjump" value="{$page.page}">
                <div class="input-group-append">
                  <button class="btn st_pjump_button" type="button" title="{l s='Jump to' d='Shop.Theme.Actions'}"><i class="fto-search-1"></i></button>
                </div>
              </div>
            {else}
            <span
              datatext="{winamic_linkobfuscator::base64url_encode($page.url)}"
              class="datatext page-link {if $page.type === 'previous'}previous {elseif $page.type === 'next'}next {/if}{['disabled' => !$page.clickable, $pagi_class => $is_product_page]|classnames}"
              {if $page.type === 'previous'} aria-label="Previous" {elseif $page.type === 'next'} aria-label="Next" {/if}
            >
              {if $page.type === 'previous'}
                <i class="fto-left-open-3"></i><span class="sr-only">{l s='Previous' d='Shop.Theme.Actions'}</span>
              {elseif $page.type === 'next'}
                <i class="fto-right-open-3"></i><span class="sr-only">{l s='Next' d='Shop.Theme.Actions'}</span>
              {else}
                {$page.page}
              {/if}
            </span>
            {/if}
          {/if}
        </li>
      {/foreach}
    </ul>
    {/block}
  </nav>
</nav>