$('#comment-form-subscribe input:checkbox:not(:checked)').prop("checked", true);
If checkboxes are unchecked, manually check them, but this doesn't seem to be working.
You might have a selector issue: I'd check that the length of the jQuery object returned isn't 0. This is what I typically use:
EDIT: as @nbrooks pointed out, :input is deprecated. This might work:
$('#comment-form-subscribe').find('[type="checkbox"]').not(':checked').prop("checked", true);
:input selector is deprecated, and the rest is functionally identical.
#comment-form-subscribe? If it is an ancestor of the checkboxes, your code should work fine.