Yes, there is a theme hook that will let you alter every instance of a checkbox. The two theme hooks you'll want to look at are:
theme_checkbox()
- https://api.drupal.org/api/drupal/includes!form.inc/function/theme_checkbox/7
theme_checkboxes()
- https://api.drupal.org/api/drupal/includes!form.inc/function/theme_checkboxes/7
Sample Code
Here's some sample code, available in the API doc links I provided above.
function theme_checkbox($variables) {
$element = $variables['element'];
$element['#attributes']['type'] = 'checkbox';
element_set_attributes($element, array('id', 'name','#return_value' => 'value'));
// Unchecked checkbox has #value of integer 0.
if (!empty($element['#checked'])) {
$element['#attributes']['checked'] = 'checked';
}
_form_set_class($element, array('form-checkbox'));
return '<input' . drupal_attributes($element['#attributes']) . ' />';
}
You can override the markup returned by implementing this theme hook.