Hello,
Apart if a programmer has made HUGE changes to the Moodle code, it is simply impossible for an activity to appear in the activity list and works if there is not a corresponding folder in the mod subfolder !!! Beleive me.
Most probably the instance of Moodle you are using is not the same as the one you are browsing using ftp.
Another (very unlikely) possibility is that someone has changed the word "certificate" to something else both in the subfolder name and in all the code (why ? no idea). This is very easy to test : just choose "certificate" in the list of the activities as if you wanted to create a new certificate and look in the url of the page after that action to see if you see the word certificate (in Moodle 2.x this is something like "add=certificate" I don't remember what it was in Moodle 1.9) or another word.