Basics:License-checks are done each time the application is accessed by a user.
Having an invalid license stops the whole product from working.
An invalid license will never have any impact on Dynamics 365, it only limits the addon itself.
The problem occurs because MS CRM is using an HttpModule for multitenancy scenarios. This http module is called with an anonymous user account. This is why it fails when trying to request, i.e. the metadata webservice.