Hm, sounds like this could possibly be a bug. I wonder what happens if you visit other pages of the plugin by typing the URL directly? Do you get a message saying it is disabled? Would be interesting to see how core plugins handle this as well. Can you write a report on https://github.com/mdjnelson/moodle-mod_customcert/issues and ill look into it when possible? Thank you. 
Custom certificate (plugin)
My Certificates still appearing after plugin disabled
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