Drupal - How to update disabled modules using Drush?

I use: drush pm-updatecode --check-disabled followed by: drush @sites updatedb

The --check-disabled option was added 2014-11-04

drush vset update_check_disabled 1 -y

You can use drush for it. First, you have to get the list of all modules that you've, for it you use drush pm-list like this drush pm-list --no-core --pipe --type="module" you'll get a list of all modules (enabled, disabled and uninstalled).

After, when you get all list of your modules, you can use drush dl [modules - list] with this command drush gonna download and replace the existent module. Like he does with drush up.

The last problem is to run the update.php, unfortunately this one you've to do it for each website or you can easily code a small script that do it.