This issue isn't reproducible OOTB.
* Do you see any Console errors in Developer Tools of your browser?
* Do you see the same issue using OOTB admin user?
If it's not related to permissions, try the following steps as well:
* Enable DEBUG log level on query class below in /system/console/slinglog
org.apache.jackrabbit.oak.query
* Reload the http://<host>/<port>/libs/wcm/core/content/sites/templates.html/conf on your AEM environment.
* You will see the logs showing some query. It would be something like:
SELECT * FROM [cq:Page] AS p WHERE ISDESCENDANTNODE([/conf]) AND p.[jcr:path] LIKE '/conf/%/settings/wcm/templates' ORDER BY [jcr:path]
* Run that query in Explain Query tool (/libs/granite/operations/content/diagnosistools/queryPerformance.html) with Include Execution Time and Include Node Count checkboxes checked.
Does it show any results?
* If it does, then the query is showing the correct results. Something on the UI side could be causing the issue.
Recompile JSPs & rebuild clientlibs, and then verify whether you see the templates appearing.
https://helpx.adobe.com/experience-manager/kb/How-to-force-a-recompilation-of-all-Sling-scripts-jsps-java-sightly-on-AEM-6-4.html
* If it doesn't, it could be something to do with cqPageLucene(/oak:index/cqPageLucene). Try re-indexing it and verify whether the issue still exists. Try using OOTB cqPageLucene index and then verify whether the issue still exists.
Hope it helps !!