I took a look at this documentation article and it looks like "if you deactivate a custom form, the form does not display in any drop-down menus on the object. However, the form does still display on any object it is attached to." So you might need to remove the custom form from the objects where it still is? There's this related documentation article that might help.
If these aren't helpful, please let me know. Also, I know @Katherine Stibley‚ and @Heather Kulbacki‚ do a lot with custom forms, they might be able to give some pointers here as to what else to check. If I'm way off base, let me know!
Yes, if the form is still visible from the Requests dropdown, it must still be attached to a queue topic. You'd want to go into that request queue and review the queue topics there.