var handleCheckboxes = function (html, rowIndex, colIndex, cellNode) {
  var $cellNode = $(cellNode);
  var $check = $cellNode.find(':checked');
  return ($check.length) ? $check.val() : $cellNode.text();
}

// Then add to exportOptions.format.body option for each file type, eg:

[...]

{
  extend: 'csv',
  exportOptions: {
    columns: ':visible',
    format: {
      body: handleCheckboxes
    }
  }
}

[...]