This could be caused by a few things:
- The xpath query  used by the AEM Client Library Manager (HTMLLibraryManager) is using some index other than the /oak:index/nodetype index.
- The nodetype index is failing to get updated or is corrupted.
- The clientlibs-service user's permissions are missing.
I. Check the service user permissions
Review this article in case the clientlibs-service user permissions are missing.