Pretty clean urls module to make super friendly urls without id uses special feature called in PrestaShop "overrides". Overriding is a way to "override" class files and controller files. PrestaShop's ingenious class auto-loading function makes the "switch" to other files fairly simple. PrestaShop allows to disable overrides, or these overrides are disabled automatically in some cases (like update of the shop) or while you apply security patch (presta from time to time releases security patches). If overrides will not be enabled - pretty clean urls will not remove ID numbers from urls!
How to enable overrides again?
To enable overrides in shop please follow this guide: disable / enable overrides in prestashop