I want to hide a specific collection-type from content-manager

That should still allow you to access it from the api.

I did the same in the following plugin todo-strapi4-plugin/server/content-types/todo/schema.json at 3551a8239a0c568fa1222cb0ce333afb80cda3a5 · PaulBratslavsky/todo-strapi4-plugin · GitHub

  "pluginOptions": {
    "content-manager": { 
      "visible": false
    },

    "content-type-builder": {
      "visible": false
    }
  },

This allowed me to hide the collection from the admin panel, but I still had access to it via API.

I wonder if there is something else that is happening.

Did you test trying to get the content from before the change, was it working?